I have a shallow repository clone and using sparse-checkout of just a handful of directories. When I upgraded from git version 2.24.1 to 2.25.0 some files not in the sparse-checkout were staged to be deleted. The directory path of these files contain the Windows reserved name of "prn". Ex: "japanese/prn/. . ." Unable to un-stage these files and reset the changes. .git/inof/Sparse-checkout: !/*/ /*/directory-*/ Reverting back to the previous version (2.24.1) allowed to un-stage the files and reset the changes.