Quick and dirty module to move ALL terms from one vocabulary to another. I've tested this on a vocab of about 1500 objects, but for safety's sake it might be prudent to throw a limiter in the form's submit function limiting action to the first 1000 terms or so. It would pick up the next thousand the time next you ran it.
You can get to the form at example.com/agile_term_mover/form/move_term.