Hi @gpetrini. My most sincere apologies! I can imagine how scary it is to experience this issue on some of your most important files. If you do not want to turn Insync on again to avoid any further deletions, then I would recommend uninstalling Insync fully, then reinstall afterwards. That way, any previous config will be removed which will allow you to sync from scratch.
However, we would like to highlight that it is not recommended to sync git repositories as outlined here and on this guide. That said, we recommend setting up your Ignore Rules to exclude the git repos so we can avoid this issue from happening again.
Let me know your thoughts. 