I used to use the built in convert options in Emby server, but recently switched to Tdarr to manage all my conversions. It's got far more control/configurablity to encode your files exactly how you'd like.
It can also 'health check' files by transcoding them, but not saving the output; checking for errors during that process to ensure the file can actually be played through successfully. With 41k+ files to manage, that made it much easier to find and replace the dozen or so broken files I had, before I found them by trying to play them.
Fore warning; this is a long and intensive process. Converting my entire library to HEVC using an RTX 2080 took me over 2 months non-stop. (not including health checks)