I have a similar problem: I would like to export a lot of Pokemon from a Diamond save to XY/ORAS. The Diamond save was dumped from an original cartridge a while ago (a few years probably), but can't remember with what kind of tool, I only know I used an Acekard to dump it. Unfortunately I don't have the cartridge anymore to try using one of the newer tools.
I can open the save with DeSmuME and actually had to use the emulators' savestate in order to open the save in PokeGen. But I haven't found a way to export multiple Pokemon at once or dump complete Boxes from PokeGen.
PKHeX doesn't seem to like the save (it loads, but all Pokemon slots are just red images and the application crashes when I try to do something).
Any possibility to fix the save (probably just the wrong format)?
Or is there another tool to achieve what I want?
Thx.