I think this issue may need to be reopened:
I am experiencing this almost once a day. I have to send a SIGHUP to the process which causes the files to reappear. An example:
I have a folder with almost 900 media files. These files are large, 20-35gb each and Plex is indexing the folder. If I ‘ls’ the media folder I can see that most of the files are gone. A few remain but it seems to be random. The files are still present in the Google Drive web interface. After I purge the cache the files reappear, for a time.