I got my private/instrument at a FBO under part 61 then went to a university that was part 141. However, as stated above, generally you have to complete the whole program with you. In our case, you had to complete the instrument course (you could get private on your own). Since I got instrument on my own, I got no credit (not even university transfer credit!) and while I got to fly the commercial course, I had to get the extra hours outside and take my checkride with their part 61 examiner (they keep one on staff). I ended up being short by about 1 hour when I did my extra flight time, but they allowed me to buy an hour in the FTD.