Sure, you would take Empty, since much of the space of the "lab" has nothing to do with the actual lab. The Upkeep modifier reflects the idea that covenfolk are constantly moving stuff around inside of the "lab" interfering with flow of mystical energies during the lab season requiring expensive ingredients to counteract such a situation.
I was planning on doing this in my last saga, though I was not so ambitious. My magus had a focus in vine plants, and conjured himself a large gourd to act as a tower/lab. The plan was to construct a building around it and get it enchanted; it was essentially made of wood, so the vis costs weren't incredibly large and the lab only really takes up the square footage of the ground floor, minus the square footage of the building contained (if your GM is generous).
I think some of ya'll are confused. The plan is not to turn the Covenant into a permanent lab. The only reason for the large "lab" is so that the Structure can be opened. The actual question, "What happens to the previously enchanted rooms" hasn't even been touched.
Yes, I am well aware of Hermetic Architecture, but I find it too hard to bother with, especially since it's unneeded here, and thought it would distract people from my question. Sigh.......
Yes, you could play with the size, but, again, not really an issue, and this avoids ST quibbles about what's part of the Covenant. 36 pawns is pretty much "boundary" (Say, outer walls and everything contained by them. Easy division, but in game terms and in role play terms.)
I don't think most covenants are singular structures... So you'd actually probably have to build individual labs around all the separate parts and enchant separately to cover the whole thing. The most widespread exception would be magic- and/or trade-sustained towers without any surrounding structures, but Hermetic Architecture is much easier to work with in this case.
(Also, a note: by most reasonable readings of the rules, the covenant would not count as part of the lab, so your gigantic lab would have tons of unoccupied space, which in turn lowers the Safety immensely. And before you counter that it's okay as long as you don't do anything risky, that's actually totally untrue; in an unsafe lab, you have to roll every season you do work in there, even work that's normally safe, just to see if you botch. So have fun either spending a decade installing Virtues or knowing that if you roll a 0 your chances of avoiding a botch will be so small that even my scientific calculator just rounds to 0. For all intents and purposes, you have a one in ten chance of botching.)
Well, first, the expanded Form and Material chart in Mysteries formally uses the term "boundary", so I assume that would cover everything in the boundary of the Covenant.
As to Safety, that was covered previously in the thread. Lots of easy "Safety" Magic Items to be made, and you don't need to spend a season "installing" them into your lab. Assuming a ST with an ounce of sense, there's going to be a top out point of "unsafe because empty". You can get a Safety score of zero.
Could we ignore that lab itself for a moment?
Sit down with Covenants for a bit, and you will find that it is trivial, but ends up with certain flaws and likely a large number of 'Empty' flaw-instances.
It is not what the OP was originally asking about, but again it is a fairly trivial problem, so no worries.
How did you enchant you lab in the first place? Technically, whatever you enchant must fit inside you lab, at the time of enchantment.
This can be solved in (at least!) 2 ways:
- Ignore that bit, "a Room is obviously inside itself".
- Build a room inside a room. I did this with one character (an NPC), who build a (slightly) smaller wooden room inside his lab, which he then enchanted to turn into stone and change size. Essentially he had a lab he could gather up and put in a pocket, inspired by Skíðblaðnir.
In the first case, there's potentially a problem, one which I would have prefered to avert earlier. You cannot invest a Room, because you must invest a whole item. to invest simply a single Room in a Structure would (to my mind) be akin to investing part of the blade of a sword, ie one edge of a double-edged sword. This I wouldn't allow either.
Mind you, once you have the lab surrounding your Structure, it should be fairly obvius how that part works.
I would echo this.
Sadly, I'm not buying this. The 'Boundary' reference in the Expanded Table is merely a description (and advice on how many extra magnitudes for size you'd need). I suppose it would be relevant if you decided to enchant the dirt inside a give Boundary, but I don't see how enchanting something big suddently allows you to ignore other fundamental rules of devices.
Do you by any chance remember this thread? And within that thread, perhaps this post?
One of the two examples given of enchanted structures in Mysteries Revised is Trajan's Arena (P.99 Ar Mag. MR, sidebar), and the quote is "An arena is roughly a standard Boundary 100 paces across", so I think Boundary is quite allowable, as is enchanting the dirt within the boundary. As to ignoring other rules of Magic Item Creation, those rules allow one to enchant multiple elements as one, up to a limit of Magic Theory. So I don't see why I wouldn't be allowed to enchant the Covenant boundary, and include the dirt, stone, whatever as one of my elements. To do this gloriously stupid stunt, I, by definition, have to have a high Magic Theory. I should easily be able to cover dirt, stone, another type of stone or two, and two or three types of wood, mortar, and brick, easy, just like I could a staff with a bunch of different gems. (Oh, there's a reason to do this! Make the Covenant my Talisman!)
Wait, you're using that logic to justify the ability to enchant everything?
You'll be enchanting the people too...
Make sure nobody leaves! 
... Or jumps.
EDIT: Although the above is a joke, it does bring up a real point: If any part of the covenant is damaged in a significant way, you risk losing all your work very easily. What's that, some grogs got too rough in wrestling training and put a hole in the wall? Say bye bye to vis, months or years of enchantment, and probably the covenant's most reliable defense. And they're grogs, they'll find a way to reach new levels of incompetence and ruin everything.
An arena is a discrete structure.
A covenant is a collection of buildings, at the very least...
You're enchanting the FREAKIN covenant. Ensuring peons do not leave is child's play, assuming you have decent Mentem. Now EVERYONE acts in accordance to my whims. Or Hubris, which amounts to the same thing. BWAHAHAHA!
On the other hand, if you have indecent Mentem, [strike]everybody will be too busy staring at its breasts to obey you[/strike] you can still probably ReCo to prevent jumping and leaving. But then you have to get into the semantic metaphysics to figure out if the old grog croaking counts as breaking it or if his corpse is him enough to count as long as nobody picks it up.
Ah, no, obviously not. Again, by the rules, I get to choose the elements which make up the Item. I am aware of only one way to enchant Animate matter, and it is lost to the Order, so people, of course, will not be part of the enchantment, anymore then the Air of the lab is when I enchant a staff. Come on, guys, you're reaching.....
(And the the Arena, again, read the example. "The Structure" is not enchanted at all, the soil is. The structure only serves as the boundary, but is not enchanted. (Which would be stupid, yes? You don't want to work your audience into a frenzy......) Mind, that example opens up real questions. I assume, in canon, the creation of the Arena, and it's enchanted field, did not create riots all over Rome as the soft dirt was tracked other places. So, either the "Dirt" was enchanted, but there's an amount that can be taken from the area before the Enchantment is lost. How much? Or, the area of the boundary has been enchanted, and "dirt" can be brought in, and taken out, at will. Sounds like a real promising place to get a Breakthrough on Auras........)
I've always found that example to be a bit henky.
Serious question as to how one handles removing dirt and how/when it affects the enchantment. YSMV.
I'm open to the idea that you can use Boundary to enchant the soil - but that will still not give you enchanted building, just enchated soil.
That aside, there's still this:
and
thus device effects cannot use T: Boundary. The explicit exception to this rule is Hermetic Architecture (ref TMRE, p. 98, thrid bulletpoint from the top, under Investing the Effects), making this possible via a (mystery) Virtue which is assumed (indeed demonstrated) in the example in the box, TMRE, p. 99.
It is interesting to note that an enclosed arena could have been enchanted using T: Room, with sufficient modifiers for size, as it fulfills the definition of a Room (ArM5, p. 113).
EDIT:
PS: While a group of Boundary cannot be used as an enchanted device without certain virtue, single Structures certainly can. I have been known to argue that en enchanted lab/tower is possibly the best way to use the Talisman rules, for non-combat magi.
PPS: If you do not have the Hermetic Architecture Virtue, why enchant the whole building anyway? Especially as you arguably don't get your Verditius discount, as you're not creating the item (tower/building) for the enchantement, but enchanting something which already exists (ArM5, p. 93).
Instead, just create something smaller and more managable - a golden brick perhaps - and brick it into the wall. cheaper, easier, more extendable (as you can make more golden bricks) and you don't have to mess with the whole outdoors lab. Just use R: Touch and T: Structure.
We can argue about the rest of it all day to no point. As to your PPS, two reasons. First, because it wasn't important. The point (That EVERYONE overlooked) was "What happens when two permanent enchantments overlap. If the gold brick makes you feel better, use it. Again, what does it do about the Lab in the structure that has already been enchanted?
And if I were to do such a thing in game, why would I use a gold brick? Single point of failure, easy to steal, and lots of reasons for people to want to steal. You don't think Verditius are aware of theft, and think it's a big problem? Heck, Verditius see theft where there isn't any! (See Item Attunement, Ars Magica, Houses of Hermes, Mystery Cults). Well, good luck stealing my Covenant!
... But the air isn't part of the staff. From a metaphysical standpoint, the residents are no less part of the covenant than the buildings, so if you're enchanting the covenant, you'll need to include all those factors. Now, granted, you could choose to enchant your covenant with the highest individual part (probably your biggest or rarest-material building) rather than the whole, in which case the disconnect wouldn't break effects not tied to the s/m bonuses, but then things start to get kind of... Weird.
To directly answer the OP, it really depends on HOW you are enchanting the covenant. I don't know how hermetic architecture works, but I doubt you can use your existing "standard" lab for it, therefore you need to meet the hermetic architecture requirements. If you actually build a lab large enough to surround whatever part of the covenant you wish to enchant (such as a single large structure), then you need to build a new lab that meets THAT requirement.
Unless HA allows use of your already existing lab, I would vote for no overlap, and you end up with (and must support) two labs.
I'm not sure I follow.
I thought the problem was that part of the (covenant/building/whatever) you're trying to enchant, has already been opened (for enchantment) and enchanted. To which I repeat:
If your problem is that two (or more) enchantments are affecting the same target, I believe we've all ignored it because there's no problem. A single object/individual can be the target of any number of effects at the same time. Or am I still not understanding the point?
Actually, using a golden brick is not that hot an idea, if you can enchant the effects you want in a single season each. Then just invest each effect in a seperate stone, and then brick them up.
The golden brick is merely suggested because it has about the same Vis capacity as a fair-sized stone tower.
The heart of it, I think is the interaction between two "wholes". As you have done, a "Room" can be enchanted. It is a whole. A structure can be enchanted. It is a whole. But a structure can have many rooms. Perhaps if I change the scale. I have enchanted a gem (And only the gem) which is part of a staff. The Gem is whole, by itself. Now, if I enchant the Staff to be my Talisman, do I get to include the gem's enchantments? The Spaces of the gem? The form and effect bonuses? Does the gem get the Magic Resistance of the Staff? I started with my example because I would want, as a Verditius, to enchant my lab. Then my thoughts got large......
If you enchanted a gem, the gem is the enchanted item. It could be attached to the staff, but it wouldn't receive the shape and material bonuses of the staff unless it was part of the staff at opening. A staff to which the gem with invested effects is attached can't be attuned as a talisman unless it has been at least prepared for enchantment on its own. And when you attune said staff, it's just the staff, not the gem. IF you attune the staff, the gem doesn't get any MR. IF you attune the Gem it doesn't provide its benefits of MR to the staff, nor does it allow you to unlock the S&M bonuses associated with the staff and the wood species. IIRC, Great Talisman allows incorporating additional components into one's talisman at a later time.