Plex seems to delete files

[OttoKerner]

You must not do that.
The optimized files are linked to their originals. If you erase the originals, the optimized versions are erased too.
If at all, you must do it like that:

1. create optimized version
2. take the finished optimzed version and copy it someplace else, outside of Plex’s reach
3. delete the original file
4. update library
5. empty library trash
6. add the optimized file back in
7. update library