While the previous version did renumber the aircraft, it appears from the old code that it did not renumber the corresponding references in the flight plan.
The answer to you question is "Yes, it would be possible" but not easily. Currently, at the time the problem is detected, the flight plans haven't been loaded.
My intent was that, once you received this message, you'd abandon the merge temporarily and fix the problem manually (e.g., renumber the aircraft in one of the files in the usual manner, which would also update any FP references.)
If you see this as a frequent occurrence, I'll try to fix it later. But, right now, my main interest is getting AIFP2 stable - which I taking much longer than I had hoped given the amount of testing to which it was subjected. Please remind me in a few weeks if you think it worthwhile.
Don