I from time to time will take some of my full blu ray rips and reencode them with handbrake to H265 files. Basically replacing the MKV with a MP4 of the same filename. Well this breaks any links to these movies in virtual channels etc. I thought rescanning, pruning, and reindexing the virtual guide data would fix but it doesn't and I have to manually trash the old link and relink the new version. Is there an easier way to handle this ?
Why change the container? Just replace the existing MKV with your newly ripped version saved in a Matroska container. (You may want Channels to reindex the file to ensure its metadata is accurate as far as the details go, but it ought to work without issue.)
I'm on a Mac and use a metadata tagger that doesn't tag mkv's
To each their own.
However, Handbrake allows for setting tags/metadata when you rip/encode, and MKVToolNix allows for modifying/tagging existing files.