TLDR; Encode in place, Rescan.
I have dozens of posts on this topic in the discord.
Make sure you do not change the path/filename.ext and just rescan.
Do not encode to mkv … just rencode in place to the same location.
IIRC, this is the tdarr default.
I have re-encoded over 100,000 files and saved over 100 TB.
I never had to redo any metadata. All metadata was preserved.
You are doing too much work.