brings up an interesting thought- a bonisagus bonisnatches an apprentice, the old parens declares a wizard war and takes the apprentice back... results vary by tribunal
I'm guessing the answer would be "you are completely within your rights to declare Wizard's War in this circumstance. Just as Every single Bonisagus in the Tribunal is free to ALSO declare Wizard's War against you. All at once."
That being said - it probably depends on the Bonisagus. Reading through the relevant section in HoH:TL, it really does seem that most Bonisagus recognize this as something of a privilege to benefit the Order, and don't abuse the power. (Ie, they use the power only if the apprentice is obviously research-inclined, or has an interesting aspect of the Gift to study, or if the apprentice is being abused.) The exceptions being those Bonisagus that are doing human experimentation on apprentices and/or obviously are doing it just to save a Season or two in opening the Gift. If that's the case, the rest of the tribunal may look away as the asshat Bonisagus gets his hand slapped.
First question is whether the Bonisagus can Bonisnatch the apprentice right back... which could lead to another wizard war, etc...
It could get resolved with certamen, or in tribunal, with one of them eventually giving up, one of them dying in the wizard war...
Well, when the WW is ongoing, the Code of Hermes is voided - so, sure: either can steal/kill each other's apprentices no problem. After the month is over? Again, sure - the Code is back in force, which allows a Bonisagus to take another's apprentice. But if the mage in question won the WW without killing the Bonisagus, then he could probably have extracted an oath out of him (and/or a few arcane connections, and/or his current research) to hold hostage over him, to prevent him from doing so.
Although the Gernicus in the tribunal would probably be working to prevent it from spilling out into a larger Wizard's War - so in this case, the end result would likely depend on the context.
It will probably vary between tribunals, much like the rules for establishing ownership of vis sources, or what counts as "magical power". There is also the special protection given to sanctums to consider. Consider a situation where a magus leaves a book in another magus's sanctum. Does the forgetful magus have a right to recover that book? If the second magus brings that book outside his sanctum then what can the forgetful magus do? Did the book's ownership revert to the forgetful magus? A tribunal could easily rule the results of a wizard war follow a similar pattern.
To put it another way, if the Code is suspended why should the Code care what happened during the Wizard's War. A tribunal could decide that if a book happens to travel from one sanctum to another during the War, then its just like any other book that somehow traveled sanctums by some other innocent means. If a Faerie decided to move the book would that cause an ownership switch?
For familiars, unless you also sever the bond the bond still functions as a clear source of magical power, and many magi will be biased in favor of protecting their familiar companions as well. (Seeing as how they are the only True Friends a magus will likely have.) A tribunal could easily hold a familiar is an extension of a magus.
Also don't forget that holding trials by direct democracy may not result in fair results dictated by the rule of law. If the majority of the Magi in the tribunal have a strong reason to dislike you, or fear they might become your next target they could easily find some reason to March you.
Summary: The rules will vary by Tribunal.