We identified a bug in GitHub sync, which may inadvertently remove files on commit for sites with a large amount of files. The bug has been resolved, but you may need to revert your Git history to undo this commit and restore your files. You can follow these instructions to revert: https://github.com/blog/2019-how-to-undo-almost-anything-with-git
Please get in touch with firstname.lastname@example.org if you have any questions. Sorry for the inconvenience!