I hope this explanation helps and isn't too technical.
Thanks for trying ;-) Let's just say the fixed memory address and absolute-address make it a bit hard to understand the problem. But guess I'm looking at it from a "simpeler point of view".
But I suppose it means that if you read the ROM and dump the info, the links inside the ROM are pointing to a certain "adress", so if you put the code at another adress it won't work anymore.
But then, if you know the correct location, and the intention is to "recreate" the ROM or in this case a merged 1.4 + 3.1 ROM couldn't you dump the files in RAM or disk, then "disasemble" it, and reprogram it a bit or put it back in another ROM and have the correct adresses again ?
Well, I did say I'm looking at it from a very different and simpel POV.