You kept a backup of the map, not used in a scenario, right?.
Once troops are laid on a map when creating a scenario you can get side effects. Therefore any complicated map should be saved as a separate map file in case of hiccups. Naturally, when hiccups occur - then its the file you
didn't back up it happens with
!
Try - delete all troops for both sides, change scenario to a meeter, then auto-deploy all for both sides (each will have an HQ left). That may do it. In fact - you may not need to delete the troops, changing battle type and redeploying all with auto-deploy may be sufficient.