It might have to do with the change from the old to the new movie scanner and agent.
VOB files were never officially supported in the first place, because of https://support.plex.tv/articles/201426506-why-are-iso-video-ts-and-other-disk-image-formats-not-supported/
if you put this into a .bat file
for %%f in (*.vob) do (
REM replace with 
REM for /r %%f in (*.vob) do (
REM to do it recursively
        echo %%~nf
         "C:\Program Files\MKVToolNix\mkvmerge" -o "%%~nf.mkv" "%%~nf.vob"
)
Try it on a copy of one of your smaller folders first!
I take no responsibility for any mess-ups.
You’ll have to remove the .vob files manually, afterwards.
If all your vob files have only one audio track, in one and the same language in them, you can also add the language tag in the command line. See How to remove tag spam and set language in several MKV files at once for more scripting goodness.