At some point Lydia was completely falling behind and got sort of stuck trying to fight an enemy that appeared to also be stuck in a wall (I'd be outside hearing exactly where she was but it was inside a wall... at a fort.

So I went far away, started going to other places but lydia wouldn't show up. I had given her a lot of stuff, and for sure she wasn't dead.

so I used to console command to place her at me (afaik that doesnt revive her or otherwise cheat, right?)... how can i find out if my save is flagged for no-steam achievements now?

I used TCL to get unstuck once and I've since gotten achievements with the character. In FONV if you used the console it disabled achievements until you exited the game, it wouldn't surprise me if Skyrim operated the same way - although I don't know for certain.