Although I somehow managed to make a playable hot seat file from a QB map, it does appear that altered QB maps, or even scenario maps can't be saved as PBEM files. I've tried many combinations, including saving them and exporting them to the QB folder, changing the file extension, etc.
The purpose of asking the question is to find a way to have more units available to deploy in QB games, besides getting rid of rarity or increasing force adjustment, which only affects one side in PBEM. In a regular CMBN game, my opponent and I would like to have huge maps with huge forces to deploy. If anyone knows a way around this, a reply would be appreciated.