EDIT: https://github.com/gwen-lg/subtile-ocr is better than https://github.com/ruediger/VobSub2SRT Subtitle-ocr had no issue with recognising "I" as "I" while vobsub2srt constantly sees "I" as "|" and blacklisting "|" causes "I" to be recognised as "]" and blacklisting "|" "[" and "]" just leaves a blank space so thanks for the recommendation! I'll be using that to convert VOBSUB to srt instead

for f in ./*.idx; do
    subtile-ocr -l ger -o "${f%.*}.srt" "$f"; done

And then https://mkvtoolnix.download/ to remove any unwanted subtitles from the mkv files

for f in ./*.mkv; do
    outdir="nosubs"
    mkvmerge -o "${outdir}/$f" --no-subtitles "$f"; done

Finally, I merge the srt files with the mkv files

for f in ./nosubs/*.mkv; do
    outdir=addedsubs
    g="${f##*/}"
    mkvmerge -o "${outdir}/$g" "$f" --language 0:ger --track-name 0:German "${g%.*}".srt; done

Once the files in the addedsubs directory look good, I delete all of the other files. You can add it all to a bash file or make an alias or both and run it wherever

MKVToolNix Batch Tool should be able to do it automatically, assuming the subtitle format is supported.

If you arent afraid of remuxing: use mkvtoolnix
Optionally has a GUI.

Juat so you know: If the name is identical to the mkv + the suffix .de.sub some media libraries automatically detect them and you can use them as is without altering the media file.
Jellyfin for example lists the file as "Ger Sub - External" in the subtitle list.
Just make sure to stay consistent or use sonarr/bazarr instead.

Console batch file for mkv merge should do that as long as subs are named same as video files (or something consistent like that name +subs).

You’d want to target the sub files not idx. If that fails I’d just do an intermediate step of merging the sub and idx files into an mks file then merging that into the mkv. The gui only needs the sub files added. I’ll try and come back to this though someone else already posted a script that should be able to be adapted to do this.

MakeMKV can do that for you.