At the rate plex breaks thing i would NEVER let it touch my libraries to make perminant changes…
That said here is what I do… not right or wrong just one way to skin the cat and I have enough storage to pull it off … all my storage is backed with ZFS and I have at least one full backup of evertthing that is also protected with parity against bitrot
I keep original content… full DVD rips in VideoTS format in a seperate folder and when plex abandoned this format began converting my base images in MKV format and only choosing to archive the main movie with only the audio that I need… i.e. No directors comments etc.
The reason
If I want to automate then process in the future to convert these archive videos to another newer format… loooking at you 265 hevc when that becomes mainstream… I can automate it without having to babysit it selecting the correct versions etc
I will keep the videotc folder off line since the server will never use it buy I always keep the source files
For blu… I started in the mkv container and only kept the original movie… so same as my transaction for DVD sources above
ALL my movies get converted to h265 with handbrake and I currently use the ATV3 preset… its quick, gives a picture up to 1080 (or source) properly cropped for source anaimaphoric … at source framerate with both AAC and AC3 multichannel with the latter as passthough… a VERY good trade off…
AND I alway have the original in MKV format if I want to play a higher bitrate version.
The ATV3 m4v files I don’t have to dick with the broken and slow plex sync either, I can copy them straight to my iPhone or ipad and they will play just fine in the navitve movie app… bypassing all of plex’s security bullshit while on the road
If I want to sync something while on the road… I still can and the m4v format is light weight enough that transcode is lightning fast and in some cases it only changes containers since the content is native for the device but plex sometimes insists on transcoding to save space and further optopmize for the device… which is a waste of time… but so far not giving users the option for force direct sync without transcode… which we have been asking for…
Bottom line… you should, if you can afford the storage to save the original version… and save the original in mkv format that plex can use if you want that level of quality ONLINE.
Have a unified format that you know works pre transcoded so that you can transcode them with handbrake or something else where YOU control the quality… then ther server has less work to do when watching content and you know what you are going to get out…
Now the server only has to worry about clients that are wireless or remote that have bandwidth issues and plex needs to move the stream down in quality to fit the outliers…