I thought I had added more detail but could not find it when I went back.
Initially I had a CTD. This left all saves but the last auto save un-loadable. That save did have a crash site on the map but could be loaded. Any subsequent saves made however would crash on load.
After wandering around here I found the XML fix for rapidfire, applied that, deleted all my save files and started over.
2 subsequent CTDs on shooting an alien resulted in no loadable saves at all.
Recently I removed all existing Xenonauts files, unpacked the zip from scratch, applied the rapidfire xml patch and kicked off a new game.
I have been careful to wait until there are no craft in the sky when saving. A while into the game auto saves stopped saving (I'll add the game date they stopped later). I still get maps with aliens that do not update from 0% chance to hit and shooting them still CTDs but so far my manual saves are still usable.