I'm not sure what (or maybe when?) you mean. This started when I was doing my first file conversion, 20 files from dsf to aif. My main music libraries and files are on an external drive at S: Music\CDs, S: Music\HiRez PCM, S: Music\DSD and S: Music\LP Rips. I copied 20 files from S: Music\DSD to Windows directory This PC\Music\Swap and back to S: at S:Music\Working. I set up the JRiver conversion source and target folders at S:Music\Working and S:Music\Test, repectively. I then carried out the file conversion. I created a JRiver Library named Test at S:Music\Test and one at S:Music\Working named Working for A/B testing. I loaded Test library, listened to a few cuts, then loaded Working library to A/B them. When I went back Test library JRiver said it was empty. I checked in File Explorer and the only files in S:Music\Test were the little JR library ones, plus the Cache folder. I then checked S:Music\Working and it was the same. I then checked the folders holding the music files for my full collection (the afore-named S: Music\CDs, S: Music\HiRez PCM, S: Music\DSD and S: Music\LP Rips). All files were still there. I immediately disconnected the S: drive.
I have an internal store drive D: with folders of favorite tunes. They are named similar to my main library folders - D: Music\CD Favorites, etc. I created a folder D:Test and library to match. As previously, I swapped a file into D:\Test. I pulled File Explorer and JRiver side by side, loaded tyhe Test Library with a file and played it everything worked fine. I cleared the Test library and watched the music track vanish a few seconds later. The same thing happened when I changed to the Main lbrary, and when I closed JRiver. The same thing happened when I repeated the effort at This PC\Music\Test. The missing files were not in the recycle bin and I could not find them with any kind of search. The files are nowhere.