Plex seems to delete files

Plex is saying it’s not possible. But when I finish optimizing files if i drag them over to the main folder and resync after removing the avi version of the files it seems that sometimes the files disappear (one directory even disappeared) this includes the newly created files.

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
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