So update does not pull erpnext and frappe from the repository, you should expect to see something like this:
INFO:bench.app:pulling frappe
INFO:bench.utils:git fetch --all
Fetching upstream
Fetching origin
Your logs/* may give clues to the source of the problem.
You may need to uninstall and reinstall those apps - or even uninstall and reinstall bench for example Bench not working