FLAC is not in the BD spec, so...

1) Extract the FLAC using MKVEXtractGUI2

2) Convert the FLAC to WAV/(L)PCM or DTS/AC3. Depending on the length of the files, it may be over the WAV 4GB limit. Reduce bitdepth/channels/don't use PCM/use a tool that ignores the header length.

3) Remux & author.

Issues===

Depending on if you want to join the mkvs, i'm not aware that tsmuxer can mke a BDMV from 2 mkvs unless they're joined. If you want to join them, make sure they're exactly the same codec & settings (and even then it may not work).

Joining 2 FLACs via mkv and then demuxing that will yield a broken file. convert to another codec 1st.

We assume your mkvs' H264 track conforms to BD profile & settings. If not, you need to convert that too.