tl;dr: git checkout master does not switch to master branch, gives no error or any output at all and I have no clue why. Any other branch works
The accepted answer (renaming the folder) works. If you don't want to do that, here's a work-around that I tested on git version 2.14.1.windows.1.
Delete the offending folder.
perform git branch
perform git branch
perform git checkout -- . to undo the deletion.
Now you can switch to and from your desired branch without issue, even with a with a folder in the repo that's named the same as a branch. You'll notice that the branch appears in the branch list if you perform git branch