Field values added programmatically dispear after a certain time
(Re comments)

That's the reason then. Those fields being in state, which means drupal thinks they were deleted and is trying to delete conent in them.

Remove them from there. Probably OK to drop the whole rows, check all the other fields in there. You might have some deleted field tables that you need to clean up manually.

I've seen someone else have this problem, what we couldn't figure out is how it happened. Please open a core issue (probably critical) and try to describe what you did.. delete fields, config import, create through manual config import. Anything you can think of that might have caused this.