I am using Git Extensions for connecting to GitHub. Recently I have faced there are files that are flagged in unstaged changes. I cannot reset/delete files. The only way to get rid of them is check-in the files.
Had the same problem and in my case it was caused because someone in my team added the '.gitattributes' file with a line:
* text=auto
Removing this file and checking in the pending changes solved the issue.
There are other posts about that can help: Discard changes in Git and Git line endings