Well, that's good. Although still leaving rather a lot of unanswered questions...
Who blocked off the tunnel? Why? Why do the fountains have such an impact of the aura?
I don't think there's much of an obvious way to progress on those questions, though, so are we ready to wrap up the thread?
Given the timing of the blockage, the most obvious conclusion is that the attackers blocked the aqueduct. Their likely motivation would be depriving the covenant's magi of a little bit of aura. The effect would have been marginal, but then, blocking the aqueduct didn't take much effort. The loss of water might also have affected any magus who relied on Aquam for combat magic, but you don't know that there was any such magus at the covenant (of course, you don't know that there wasn't, either).
Why do the fountains have such an impact on the aura? Well, the answer to that question is obvious once you understand the nature of the aura. 
But yes, that should wrap it up.
Scott
Oh, there is one aspect I neglected to mention: the running water qualifes as one of the covenant's two Healthy Features, especially as the plumbing system includes sanitation.
Scott
Great. I've been assuming the Hypocaust is the other Healthy Feature - if only it was in the lab of someone who wasn't a Weak Enchanter and therefore had a magic item investigation total above about 10.
Good assumption, considering that I only figured that out today (though actually, I may have decided that some time ago, and forgotten about it in the meantime). But yes, somebody is going to have to figure out how to use it.
Scott
Do the Magi know for certain that the Hypocaust is fully mundane?
I ask as if it is fully mundane and in disrepair it could be fixed. Then perhaps the goal is to "automate" the amount of effort required to keep it running. I've read that hypercausts took a huge amount of effort to keep going, and magic can help with that.
That might be better thematically for the covenant that what I was thinking about for heat and light devices.
I'm pretty sure the Hypocaust is a magic item (I think Tasia detected it as such) - the problem is none of the Magi know the trigger to turn it on, and nobody's spent the necessary season of investigation to work it out.
Yes, it's a magic item.
That being said, it won't provide light, and it doesn't help Viola's lab, so post your ideas in the Covenant Development thread.
Scott