DragoonClawNZ said:
You can get the chapter times from the .mpls file under TSMuxer and then (I haven't tried this) add them using MKVMergeGUI under 'Chapter Editor'.
That's right. In tsmuxer, you check the custom chapters radio button under the Blu-ray tab and then import the mpls. Alternatively, eac3to can generate a text file for the chapters from the playlist and if you go to mkvmerge's chapter editor and load that text file, it seems to import the times successfully.