Just a suggestion, but instead of converting and deleting the ROMs every time the emulator is ran, how about putting an option in tools to covert ROMs with a source option, and leave the ROMs in the source folder but put the converted ROMs in the destination folder?
That way ROMs would not have to be deleted or converted except when the end user chooses?
Again, it's just a suggestion...
BTW, what arcade games are supported? A text file included with the emulator listing supported ROMS would be nice...