I rarely have success with make clean and make apps after some time of development, branch switching etc. The issues are mainly related to python packages missing.
Sometimes it helps to move some out of "desktop/core/ext-py" for make apps to be able to move forward. Other times it just fails with a cryptic message and I feel that I waste time trying to figure it out. If I can't solve it I resort to a fresh clone from github and it works again. A fresh clone also means I need to spend time setting up git, db, ini etc.
It would help a lot if make clean would actually clean it to a state similar to a fresh clone in terms of python dependencies.