If it happens again, I'll try the things you all have suggested, thanks! ( I wish I would have kept the corrupted map for testing purposes!)
EDIT:
This happened again, and I figured out the problem.
It's caused from overly-complex brushes or just a shitload of complicated geometry (i got this in my mobius map). Here's some fixes... all of these work independently:
-Under CSG run with "-cliptype precise" switch.
-Make the complex stuff func_walls
-I dunno if the copy/paste method Tetsu0 mentioned would work... I wish I would have tested it! (Again, I didn't save the offending map for further testing purposes like a moron).
-obviously, you can remake the whole thing! = )
Hope this helps somebody!