Not sure that Identify will cover every possible abnormal use of a magic item. Bag of Holding(BoH) and Portable Hole(PH) are designed as stuff holding devices. I would expect that Identify will return normal information like how much crap it will hold, any size/weight limitations on said crap, types of crap that can be stored, how to get crap into/out the thing. Being turned into a plane shifting device if combined with different stuff holding device may well fall outside the realm of information that Identify provides.
If a polymorph potion is Identified, I don't think Identify will return the complete list of possible potion miscibility effects. Just the info about what happens if you consume the polymorph potion. Mixing a BoH and a PH are a form of item miscibility and IMO, outside the realm of Identify.
I really think that the original ruling about plane shift and loss of items was to prevent the use of a PH full of several BoH to create a near infinite storage system. Not to create a standard use combo plane shift grenade. Would not be out of line for the GM to rule that putting a BoH inside a PH results in a pile of stuff as both things empty before falling inert to the ground. Or some other interesting but not plane shifting effect.
But as OP mentioned, the situation is dire, maybe the GM will buy off on the effort and resultant cost.