If it lists the files under the "to be committed" section, then just proceed with the commit; the files will remain deleted. (Git tracks deletions too, not just changes.)
If it lists the files under the "changed but not updated" section, then you have two options:
Undelete them by restoring the version in the index: git checkout path/to/folder
Mark them deleted in Git, then commit: git rm -r path/to/folder
I was also having red colored deleted files when I took pull from upstream/master. I tried different things but nothing worked.
Eventually, I had to revert all changes (committed, staged, unstaged) for my forked branch and had to re-sync my repo with the upstream master branch.