Remuxing is what MakeMKV does. It just takes the original files, let's you remove and/or add streams and then repackage everything in a new container. It doesn't change the quality of the individual streams and is generally much faster. Ripping the files from the original disc is actually a form of remuxing. You mentioned CPU speed and the quality of the PC. Remuxing speed should pretty much be the same whether it is a computer that is 6 years old or purchased brand new yesterday since it is just moving information from one spot to another.
Re-encoding is what Handbrake does. It takes the original file and then runs the streams through and makes actual changes to the streams, usually shrinking them. It takes much, much longer. This is also where CPU speed (and often GPU speed) can make a huge difference in speed.
Whichever road you choose is up to you. I use a mix but like you said, HDD space is cheap. That's why I use RF factors of 16-18 because it generally gives me quality that is comparable to the original. I will often check the encode once it is about 20% complete or higher and do the math to get an idea of how big the Destination file is going to be and if I don't think I am going to get a space savings of 25% or more then I will usually just abort the job and just go the remuxing route. Like I said, I had that problem with the Battlestar Galactica Blu-Rays. Each episode ended up at 12+ GB when I re-encoded at RF 18. So, I demuxed them using another tool called TsMuxer, created an .aac and multi-channel .ac3 file (as I showed above) using MeGUI and then just remuxed with MKVToolnix. Episode sizes were 7-10GB that way. I have noticed that re-encoding is particularly pointless when the original video is really noisy/grainy and especially when the video is VC-1 instead of AVC/h264, like several of the BSG episodes, i.e.:
The movie "300" had the same issue.
On the other side of the coin, "Godzilla (2014)" went from 22GB to a little over 8GB. I was so startled by the size that I re-encoded again at a higher RF and it still came back under 9GB. You just never know. There are other ways to save size using the Advanced Options and a 2-Pass Encode but to get really aggressive an maintain quality requires a huge amount of CPU power and time. I got really crazy with some settings to re encode "The Dark Knight" Blu-Ray and it took 28 hours to re-encode with an AMD FX-6100. As storage costs have gone down, I pretty much have abandoned the Advanced Settings and just gone with the one-pass RF 16 or 18.
You said you were having trouble with Alvin and the Chipmunks. I am not sure how you were setting things up because MakeMKV should just give you a single .mkv file with the complete movie in it. Are you ripping from the Blu-Rays playlist or trying to dig out the .m2ts file? The best way is to use playlists:
https://www.dvd-guides.com/guides/bl...blu-ray-to-mkv
With the way things are chopped up now and how they redundantly use portions of the video for different versions of the film, it's not as straight forward as DVD ripping. Use BDinfo to find the playlist you want and rip that or load that playlist into Handbrake for to re-encode.
The next thing you may run into is Playlist Obfuscation. As a way to make pirating more difficult, some BD makers have created this method of frustrating a would-be disc copier. When you load a regular Blu-ray into BDInfo you will get one or two playlists that are obviously the movie you want. If you load a Blu-Ray with Playlist Obfuscation there will be dozens or even hundreds of potential playlists and only one or two are authentic. The rest are dummy playlists and you won't know it until you play the video back and the movie's scenes are are out of order. You can usually discover the correct playlist by Googling the title and someone somewhere will have the answer. The redfox.bz forum is the best I have found for finding this info. The other solution is using AnyDVD HD. When you load a BD with Obfuscation, AnyDVD HD phones home and finds the correct playlist. It will then alert you in the info window which playlist is correct. You can also use AnyDVD HD's SpeedMenu feature in conjunction with Cyberlink PowerDVD to find the correct playlist as it will display the correct playlist on the customized SpeedMenu instead of the normal Menu.
That takes you to TV shows. When there are multiple episodes on a single disc, the correct playlists are usually ordered 800, 801, 802, 803, etc. However, they will occasionally mix it up by making episode 1 correspond to playlist 802 and episode 2 is playlist 803 but episode 3 is playlist 800, for example. I don't run in to this alot but it is annoying. I have found that the only real fool proof method for me is to load each disc up in Cyberlink or VLC and write down the duration along with the episode name. That way when I load the playlist into my ripping or encoding software I can match the duration with the episode title.
Finally, since you are playing back on Blu-Ray players you might need to know about Cinavia. Check your Blu-Rays and see if you find the Cinavia logo on any of them:
If you see it on the cover then you won't be able to play it back on your Blu-Ray player. No matter what someone may claim, there is no real workaround for this. If you rip the Blu-Ray and then play it back on a Cinavia licensed player, the audio will drop out between 10-20 minutes of playback and you will get an onscreen warning about Cinavia protection:
All Blu-Ray players that have been manufactured since February 2011 are required to support Cinavia. There are some workarounds like completely re-encoding the audio but I have yet to hear an example that doesn't leave your audio tracks sounding terrible and distorted. You can compare your Blu-Rays to this list:
http://www.cinexhd2.com/cinexdb/
I hope I haven't muddied the water too much. Let me know if you get stuck or need some further input.
Incidentally, Mezzmo supports .iso files. You could just rip your Blu-Rays to an .iso using AnyDVD Image Ripper and just let Mezzmo make playlists out of it. It is not as pretty as ripping the individual tracks but definitely works. Then you can kind of skip everything.
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