I didn't have anything like that happen, though now that you mention that I remember I did load an autosave at one point after I got spawn camped right inside a level 8 dungeon. The autosave put me back to right before I entered the dungeon I think, and that was maybe an hour or two before I noticed my colonists were missing skills.
Edit: I took a better look at the times and my older saves. I have a manual save about an hour before the one I posted where all the skills are fine. In that hour long period I mostly did base building, I attempted a single dungeon that spawned inside my base as I was building it (turned around at one point and there was a giant rock covering half my colony), both my followers died right inside and I kept dying so I decided to load the auto save, I then placed a training machine, and recruited 4 more colonists, and while I was recruiting colonists I noticed the skills were missing. So I feel like it was probably the autosave that did it.