When I wanted to fire up 2K12 from Steam I got a message similar to this:
I had a feeling that Steam was gonna do the file verification thing and overwrite all my mods, so I was hesitant to click OK and asked at their forums to see if it indeed does the verification. Turns out it does, so backup your folder before clicking OK.
I don't know if they also converted 2K11, 2K10 and 2K9 to the new content system yet but sooner or later they will, so this applies for all Steam distributed 2K games (2K13 should already be in the new content system so this doesn't apply)