First time atom deleted my files I thought my computer just bugged out.
Second time atom deleted my files I thought I opened to many active files and it made atom crash.
Therefore I downloaded backupper and localHistory addon to maybe help me if it happened again.
Third time atom deleted my entire file directory which included all my backed up files. (I did a clean install of atom the third time) I also only kept up 2 to 3 active files opened.
I loved atom for its many extensions that’s why I continued to use it even after all the problems but THREE times all my files deleted. Sorry no way I can use atom anymore.