If there are any local changes in the repository then patchtest will delete then when it test-applies the patches. (the git reset --hard in repo.py) If it insists on applying/reseting the current branch then it should _definitely_ refuse to run if there are local uncommitted changes. Ideally, it could create a temporary worktree so it can run in a pristine branch.
Patch in master to fix: https://git.yoctoproject.org/poky/commit/?id=4ba54e29ffa6e3dbfcb92752a759b805a2591a09 It logs an error to console and exits if there are local changes. The temporary worktree idea will be kept in mind for future patchtest refactors.