I see this more often than I want to, also. *Usually* if I exit from the bad load to the main menu without saving, and then reload my save, that will fix the missing stuff.
Sometimes I've had to completely exit the game and repair it to make it work right, though. But I"ve only reinstalled origin once lately, a few weeks back.
I use mods... if I'm playing, there's SOMETHING modded in it. No CC right now.
One more thing... sometimes if the localthumbcache file is pretty big, I'll delete that before repairing. I leave everything else alone, though. (Which may be bad, I'm not exactly sure... but it does seem to cause less issues for me.)