My witch farm is no longer a witch farm. It seems like the witch area has been deleted and now only spawns normal mobs .

Seem to remember something about needing to upgrade to a prior update and then explore to save things like witch farms and nether fortresses, certainly I have explored in my witch farm area in all versions the server has been in.

Could maybe be related to this bug (just a guess of course)
see the comment by Anomie X (21.08.2014 11:59). In the save data witch huts have a Y coordinate for the whole structure and one for each child. The Y of the outer node was previously ignored but now in 1.8 it is checked.
Or maybe the other thing that is mentioned in the comments there that witch spawning is now only possible from Y 64 to 71 (always true for newly generated huts but maybe not for older ones)