So I played the game for 9 hours over the past few days, have had this frustrating save glitch. now it's telling me the game isn't even installed? What's going on?

good question, got to programfiles\steam\common and see if your fall out dir is there.

I've got the same problem, finished update this morning and then it said it was downloading all 6.72GB (the whole game), so I restarted steam and now it says it is not installed. And yes all the fallout files are in the directory.