here is a little app i put together, point it at your plex directory and it will convert all files from one type (.avi etc) to another and then delete the original file (work through the entire folder tree).
I had to convert over 5000 files and all the free programs i found put the files in a single folder meaning i would have to place them in the correct folders then delete the original.
Plex converter I have added the project to the folder (visual studio solution c#)
but .avi and .mkv are only containers… What matters more is the codec… With a simple container incompatibility it should just de-multiplex and re-multiplex the file, which takes very little resources… But if all it’s doing is that process ahead of time, you should be very detailed, edit your original post with what exactly is does and why…