This Was a post similar to yours back in 2024, and the answer is mostly, make a script using the CLI.
Fortunately I’m also in your same boat, I download a lot of anime for my media server and get its subs externally, so Ive written a few powershell scripts that merges, filters, and edits audio and subtitle tracks. It’s pretty primitive since I just recently started working on it, but I’ll keep improving them into hopefully a fully fledge app in the future.
The subtitle names don’t have to exactly match the video files. For example if you demux subtitles with gMKVExtract GUI there’s stuff added to the ends of the subtitle file names but that doesn’t matter to the batch tool.
The batch tool can simply add the new titles or it can delete existing titles and replace them. It can also delete the old video files after it’s done.