I don't think RTW/ALEX are save-game compatible, BI/RTW is IIRC. If you switch, you will get irreversible trait errors.

Is that problem with dead enemies solvable by sending your own troops away? If you still have to fight even there is no sight of an enemy unit, look out for soldiers that got stuck in barriers blocking their escape-route, this normally works for me.
Maybe other people can share their thoughts about the mentioned problems too.

XSamatan