In a repository A the folder sub is included as git subtree of the repository S - pointing to master branch.
I ha
If you used git subtree (and not git submodule) to create the subtree, then it's just a normal dir. To switch it to another branch, just delete it and recreate the subtree from the new branch. This is:
git rm <subtree>
git commit
git subtree add --prefix=<subtree> <repository_url> <branch>
That should work without problems.