Steam is gradually converting all the games on its servers to a new, more efficient format. Just let it run and it should be okay--although you may have to replace ini tweaks, re-check any mods you're running in the launcher, and any adjustments programs like SKSE made to TESV.exe. After Morrowind converted to the new system I had to reapply the Morrowind Code Path, for instance.
Other than that you should be okay, though. I've only had one or two hiccups with the conversion thing.
Oh, that's all? (sarcasm.)
Thanks for the response, I'll backup everything and let it do it's thing. "New, more efficient format," is about the least useful description of anything I've ever read.
"Why is it better?"
"''Cause it's better."
"Oh."
Alright - I'm on it.