I’m using tinyMediManager 2.9.3.1 on Win 10 (newest updates included).
I had a movie file in the main folder “Western”. Because I had it twice, I deleted it. Then I was really surprised – the whole “Western”-folder was gone, including over 50 movies, tinyMediManager cleaned it completely up. 
So, first of all I was looking for some other missing movies in other locations. Also my whole “Cartoons”-Folder was no more available. 
I got almost panic.
Fortunately I found the Folder “.deletedByTMM”. 
Everything was still there. 
So I felt very happy to be able, to recover all missing files.
So be carefull, if you delete some movies, not correctly sorted into subfolders. Check first, that your subfolders are still available …