www.makemkv.com

The three other MKV files play fine using VLC. However, Handbrake now tells me "No Valid Source Found" when I try to convert any of the three to m4v.

Romansh wrote:HandBrake has the following limitations for file-based input (e.g. MKV):

1) max. 20 streams (video, audio + subtitles)*

2) no DTS-HD support**

Both limitations are gone in the latest nightly builds.

These limitations don't apply to Blu-ray folder structures (i.e. what's created with MakeMKV's "backup" feature).
If you don't need subtitles***, using the backup feature is the best way to rip and prepare a Blu-ray for HandBrake.

Additionally, the VC-1 decoder doesn't support interlaced compression (affects Blu-ray folders too).
This will remain the case until FFmpeg's VC-1 decoder adds interlaced compression support (no ETA).

*
This limitation no longer exists in the nightly builds (as of SVN revision 4028).

**
In 0.9.5, DTS-HD audio is sent to a DTS decoder which doesn't support DTS-HD, resulting in corrupt audio output.
This doesn't apply to DTS-HD from M2TS files and Blu-ray folders, because the M2TS demuxer extracts the DTS core before sending it to the decoder.
This limitation no longer exists in the nightly builds (as of SVN revision 3785): DTS-HD audio is sent to FFmpeg's DTS decoder, which discards the HD extensions and decodes the core.
Also, DTS-HD passthrough is now possible (as of SVN revision 4055).

**
If you want to hardcode ("render", "burn in") Blu-ray subtitles, you need to:
- a) rip the Blu-ray to an MKV file
- b) extract the PGS subtitles (with mkvextract)
- c) convert them to VobSub (with BDSup2Sub)
- d) merge the video and audio from the MKV rip with the VobSub subtitles to another, intermediate MKV file (with mkvmerge)
- e) feed that intermediate MKV to HandBrake which can then burn-in your subtitles

If you want soft subtitles (in an MKV file), you can:
- a) extract the PGS subtitles from a Blu-ray folder (e.g. MakeMKV's backup), using eac3to or an eac3to GUI like ClownBD
- b) optional: convert them to VobSub (or OCR them to text subtitles, with SupRip)
- c) add them to HandBrake's output with mkvmerge (no need for an intermediate MKV file, so you can compress MakeMKV's backup with HB)

The soft subtitle workflow above involves Windows. For a Mac or Linux-only workflow, you will still need to rip to an MKV file and extract the subs with mkvextract;
but since you don't need an intermediate MKV for HandBrake you could delete the MKV after extracting the subtitles and compress the backup with HandBrake.

One way to avoid all of this for soft subtitles (extraction, conversion or OCR) is to simply use an SRT file from the internet.