No, if you swap mods, the save games cannot be compatible. Think about it, a ships model your flying with some guns from one mod in a save file that you try and use on another mod that doesn't have that ship/guns/systems.

Not a chance of compatiblity I am affraid!

by the way, mod manager doesn't delete the save games - it moves them. It makes folders depending upon the mod/combination of mods (ie - open sp) that is activated! Therefore, reactivating a mod should result in enabling playing of that mod.

Only the autosave and restart cause any problems - as they may not get moved, and you hit that problem mentioned above.

Just a little note. This forum is dedicated to Freelancer discussion, not to the mods themselves. We have modding forums for those - in specific the moding feedback (give thoughts on mods - check forum for existing threads), mod technical help (for issues your having - like this one) and also - we have a load of actual mods forums - support forums hosted for the larger mods. Rebalance has one of those forums too, so if you get questions in regards to rebal, apart from going to Mikes site at www.rebalancemod.com - you can try in that forum too!