That's normal behavior, transcoded files are deleted when has not been accessed in 30 days, original files are still in your server. When those files are accessed again, they are trans-coded and displayed. This helps to save space in your server when old files are not being accessed.
If you don't want old files being deleted, you need to edit your database or edit core files. I don't know if is there any other way to disable it.
The problem had place because there was additional (cloned) site which was connected to the same storage, pruning from cloned site deleted some images, but DB records was left on original site, this caused the issue when images was disappeared.