I wondered how those patches worked but never bothered to find out how.
Normmatt made the same suggestion I would have but if it is lacking in the modded version you have 2 choices:
1) Hope the command line is still there and dump the ram (it will be 08000000 through to 09FFFFFF (for a full 256Mbit rom, cut it down accordingly for smaller roms). I can not seem to find a command line list for VBA right now but I know they exist.
2) Use a windows hex editor to dump the memory. Same principle applies, you will need to find the memory location of the emulator and then the location of the rom and then dump 32 megabytes (or however big it is).
There is an outside chance that the ram is compressed or obscured but I will save the reverse engineering parts for if that happens.
You could also just dump the entire memory section associated with the app and pull the rom out (I doubt the initial header will be changed and it will likely all be at once