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

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.

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

MakeMKV can do that for you.