MakeMKV can rip straight to .MKV files so you don’t need to use handbreak at all unless you want to compress it.
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Does that mean it is lossless, if you rip to MKV with MakeMKV?
Yes it is lossless.
Yes
That is correct.
I have in fact never used MakeMKV in that way, I've always used the backup option. That makes it a lot easier, thanks so much for pointing me into the right direction!
Usually what I’ll do is I’ll recombine the folders into an iso file using mkisofs and then keep the ISO as it keeps all the menus and everything in tact. Later if you want, you can run that ISO through MakeMKV and just rip out an MKV of the main title through. But since I have enough disc space I just rip all my DVDs and BDs to straight ISOs to keep all the menus and extras in tact for later.
Drag the main BDMV folder that has stream and playlist subfolders into handbrake. It will read the playlist files and show you possible combinations that you can choose to encode from. It will also grab chapter and subtitles.
At least it should. Though makemkv as others note can do this itself.