IMS, the winter covenant the PCs joined includes a Bjornaer maga who hasn't been seen for four years. She was always fairly reclusive, so at first this wasn't unusual. Now that the years are piling up, the characters are wondering if she's dead or in Final Twilight. While I know that answer (the advantage of being primary SG), it's raised a question that I can't answer - how do you know if a missing magus is in Final Twilight? Or from the players' perspective, how long do you wait before taking over the maga's lab and parceling out her books and enchanted items? Since the duration of non-Final Twilight is effectively unlimited, I'm not sure how long would be a reasonable waiting period.
In one of my games we noticed a sudden problem with a magus's familiar. We don't know if it's from his death or final twilight. Regardless, I would think either would severe the familiar bond, leaving the familiar in a bad state. Of course, that doesn't help with a Bjornaer. I suppose, since many Bjornaer become their Heartbeasts and lose their intelligence, you might look for the Heartbeast. There are probably some good related ideas. Seems like a good opportunity for the players to do some clever investigation.
Break The Code and scry on them and hope no one cares, that's about it. If the mage is in trouble and his sodales come to his aid, one would think/hope that any scrying might be overlooked - but some magi (or Players) can get weird about that, and it could even become a point of blackmail if the mage has a leaning toward such power games.
It only gets worse if the missing mage is lost/trapped in a Regio - nothing to say definitively if (most?) scrying spells even work in that case.
If they were smart when writing their Charter*, there's a clause about "What to do if/when a mage goes missing" - if not, their only choice is to take assume any risk upon themselves for their actions. If they divide up his swag and a century later the missing mage shows up again, technically, by The Code, that becomes "theft" and can be prosecuted as "depriving of magical power". The only defense at that point is "Oh, be reasonable!" - which is not the most reliable.
(* If the "Players" wrote up the actual document, and especially if, in character, they consulted a RedCap or Quasitore, there is a solid argument that their Characters would have known to add something about this obvious possibility - and a generous/merciful SG could let them add it in after the fact, since (to a mage) such a contingency should be a standard consideration. Otoh, some SG's cling to the practice that if the Players didn't say their Characters lit their torches, then no torches are lit, not even a bureacratic one.
However, Players should add such only after due consideration regarding the waiting period - if their own magi get trapped/delayed, they don't want to show up to an empty lab and sanctum. 7 years without communication always struck me as not an unreasonable length of time, but it's purely up to personal preference.)
The Base duration of Twilight is 7 years at Warping Score 8, 7+stress die years at Warping Score 9, and eternal at Warping Score 10. Thus, I would not even start thinking about Final Twilight before a dozen years have passed. To have 90% certainty, you'd have to wait more than 16 years. To have 99% certainty, you'd have to wait more than 27 years.
Now, the PCs probably do not have exact knowledge of Twilight mechanics. Still I'd say anyone with Magic Theory 1 has a good chance of knowing that it's not uncommon for elder magi to return from Twilight after more than a decade, and that there have been cases of magi returning after two or three decades.
As Cuchulainshound says, you can always scry to find out. Although that may be legally problematic, and if they are a senior magus with a large Magic Resistance might not be practical anyway.
However, the issue has surely arisen before, so the Tribunal should have a precedent about what to do. Also, something to consider is whether another magus is holding the voting sigil (i.e. the proxy vote) of a "missing" magus. Trying to prove that missing magi are truly dead or in Final Twilight might well be frowned upon.
Generally, I would think it should be something like "if the magus isn't heard from in x Tribunal cycles, in the abscence of contrary evidence, a magus can be assumed dead or in Final Twilight." As a Tribunal cycle is seven years, four years would probably not be considered long enough to wait. How long to wait might depend on how long-lived magi are in your saga. If magi live for a really long time, then seven cycles of seven years (i.e. 49 years) sounds like a good number. If magi live quite a short time (usually only say around 100 years) then maybe two cycles of seven years (14 years) would be long enough.