Can this be done by editing the meta file and .bat file when running in batch mode?
Thanks for your time.
I do this all the time (mostly for movies that have two forced tracks).
There is likely a better way but I just let it complete the remux. If I discover an issue I delete the remuxed files, edit the line out of the meta file and save it (your example shown below). Then I open tsmuxer.log in a notepad (notepad++ actually) and copy the entire command line including quotes. Next I open a command prompt paste the copied command line and let it run.
MUXOPT --no-pcr-on-video-pid --new-audio-pes --blu-ray --vbr --custom-chapters=00:00:00.000;00:00:21.104;00:01:52.738;00 :07:55.350;00:09:55.970;00:11:18.761;00:13:24.178; 00:14:49.806;00:17:14.242;00:20:40.948;00:22:25.30 2;00:25:12.886;00:29:32.813;00:31:41.483;00:35:51. 733;00:40:48.571;00:44:16.320;00:52:04.580;00:55:0 3.842;00:58:27.921;01:02:27.702;01:05:33.012;01:10 :06.911;01:11:17.940;01:16:20.951;01:18:08.100;01: 20:26.363;01:24:18.178;01:26:44.783;01:29:54.723;0 1:31:02.415;01:33:08.541;01:37:21.419;01:39:06.315 ;01:42:33.731;01:44:41.567;01:46:19.248;01:48:07.7 31;01:50:24.952;01:56:47.667;01:59:13.063;02:00:31 .391;02:01:21.316;02:02:23.378;02:03:56.971;02:05: 15.133;02:06:25.995;02:07:23.177;02:08:28.993;02:0 9:53.536 --vbv-len=500
V_MPEG4/ISO/AVC, "E:\BluRay\Video_2.h264", insertSEI, contSPS
A_DTS, "E:\BluRay\Audio_3_English.DTS", lang=eng
S_HDMV/PGS, "E:\BluRay\Subtitles_9_English_FORCED.sup", lang=eng
S_HDMV/PGS, "E:\BluRay\Subtitles_4_English.sup", lang=eng