Remuxing can butcher a conversion, and is just an unnecessary step if you’re not skipping commercials.
It works fine most of the time, but it has it’s issues. Occasionally it sets the wrong framerate, or colorspace. At one point i noticed some of my conversions were skipping frames. Looked at the metadata and the framerate was something like 29.6 instead of normal 29.97 etc. Adding --cfr or turning off remuxing fixed the problem, so no big deal… I missed it in my testing, so went ahead with a long batch and had to redo like two weeks worth of conversions. I still had the source, so again - no big deal, but very annoying.
The biggest problem with remux is subtitles. By default, the scodec is ignored in the remuxer so the only way to get subs is by triggering ccextractor, which itself works fine most of the time, but has its issues. There is currently no good/easy way to work PGS subtitles, which are becoming more and more common on blurays etc. PGS are better off passed, not worked, and remux doesn’t offer a way to pass them while ccextractor doesn’t offer a way to extract them - so basically no PGS with remux.
I actually tried to remedy this yesterday by butchering the config file and changing the default
CopyRemux0=-i -ss 0 -vcodec copy -acodec copy -map 0:a -map 0:v -f mpegts
CopyRemux0=-i -ss 0 -vcodec copy -acodec copy -scodec copy -map 0:a -map 0:v -map 0:s -f mpegts
This helped a bit, but apparently mpegts has it’s own limitations on what kind of subs it likes and doesn’t like, so it didn’t work on all my files (no subs were passed to about 4 out of 12). So i tried this
CopyRemux0=-i -ss 0 -vcodec copy -acodec copy -scodec copy -map 0:a -map 0:v -map 0:s -f matroska
This was almost a success. Out of my 12 test files, 11 converted just fine with all the proper subs etc. The one that failed thew up an error about incorrect input color space. I am sure if i do some digging around i can find the params i need to fix this, but at some point you have to ask… why ?
When not skipping commercials, the only real advantage i see in the remux is the fact that it gives me a local file to work. Outside of that it’s just not needed. It can create wacky errors (frame rate), it requires a use of a third party app for subs (ccextractor), and doesn’t allow PGS at all. And overall, i just don’t see a point. My source is mkv, and so is my output, there is just no need to go through an intermideary format (ts). My handbrake profile passes subs without issues, never messes up framerate or worries about colorspace when working the mkv, so why bother ? I mean, i’m sure it makes sense in a whole lot of situations, but in mine - i would rather just copy the source, and work the source mkv off the local temp.