Hmmm, it's the first we hear of this. The only way folders can get deleted from within ComponentFinder is if you specifically right click on a folder in one of the open tabs and then select to delete it. There will then be a warning, asking if you're sure.
Can you send me your log files located at: C:\Users%USERNAME%\AppData\Local\F3d_FlexTools\logs
Please send as a zip through the contact form at: https://flextools.cc/contact