The reason for asking is that I’ve been removing some “Closed Caption” subtitles from some of my media and one of the side effects of doing this via ffmpeg using -bsf:v filter_units=remove_types=6 is that it also removes this encoding metadata from the video stream.
No, most likely not. Because only if the encoder put them there, they are present. I’ve encountered many files which were encoded by various app, where this information was missing. Some were even patched by people to present a wrong H.264 level.
However Plex’s deep analysis will still be able to determine e.g. how many reference frames the stream is actually using, and to what H.264 Level it is conforming, even with the above information missing.