Oof, this isn't something that should happen, and it definitely isn't something I've seen happening before. But there's definitely a dirty fix I can think of that would certainly keep it from occurring. Sadly I probably can't fix your save, I know nothing about save editors.
The best I can recommend is you take a break until my next update which puts in a few extra preventive measures for bugs like these that have been reported but which I haven't been able to replicate. Hopefully preventing them altogether.
Sadly the release of this update rests largely on my artist who has been quite busy and as such has been taking a while... Until then I can't release patches as the developer build has a number of unfinished scenes that make no sense without the art. I'm sorry.