Track of "Clean" files doesn't work

I don't know what's happen, but I loose lots of files in my project. There have "Clean" status in "Unstage" section in the Sourcetree and I can't stage and push them to repo or move them to other section. It means that I can't work with my Bitbucket repo anymore.

This is also no docs about "Clean" status and nobody knows what is it https://community.atlassian.com/t5/Sourcetree-questions/What-is-quot-Clean-quot-files-and-how-to-stage-them/qaq-p/1821758