Ack -- water soluble dyes, right. Never mind...

I'd expect the gelatin to stay stuck through processing if you once get it stuck, certainly; it takes *days* of soaking to free two negatives that get stuck together by drying in contact, if you ever manage it at all. But you would certainly get some bleeding around the edges, and the dampening to get the gelatin to stick would likely cause some pain with the dyes too. Dichromate bleach will decolor a lot of dyes, too.

I suspect the only way to tell if it'll work is to try it.

Otherwise, I don't know what glue you could use that will leave the film flexible, not add too much thickness, and dries waterproof. Silicone caulk comes to mind, but it's almost impossible to spread thinly enough, not to mention its transparency is only so-so...

Might actually be simplest to use a pin registration system. They're accurate enough, if the pins aren't worn smaller than the punches...