Oh this really bums me out but I restarted my game and after goofing around in Skalitz for a while to see what works and what doesn’t (lockpicking is “better” but I never had an issue before).
I did a couple of manual saves to see how reloads are handled and found some strange behaviour (could not interact with doors, etc) but then did a “Save and Exit to main menu” before going to bed. Woke up this morning to play some more before my son’s baseball practice and found there was no exit save file and it reverted me back to my last manual save.
Lesson learned but a temporarily sad Kickstarter player at the moment.