Small update: Had weird issues with audio cutout when seeking to certain parts of the resulting video using the ffmpeg command I stated above.
Leaving out subtitle tracks did not have this issue. Turned out that adding
-max_interleave_delta 0
solved this issue when copying subtitle streams.
Error was present when muxing in srt subtitles, while vob subtitles worked fine.
Final command used for dual audio multi-sub film->ntsc anime files:
.\ffmpeg.exe -y -r 24000/1001 -i ..\upscaled_frames\frame%08d.jpg -i '.\input.mkv' -map 0:v:0 -map 1:a? -map 1:s? -c:a copy -c:s copy -c:v libx264 -r 30000/1001 -pix_fmt yuv420p -max_interleave_delta 0 output.mkv
Hope this helps anyone upscaling dual audio and/or multi-sub anime that is running into odd results.
Note:
-map 1:a? basically wildcard maps all audio tracks from the original video file, same for 1:s? for subtitle tracks. The ? ignores the option if no tracks of that type are present, i.e. no embedded subtitles.