I ran a test and didn't have this issue, unless I'm missing a step? I don't usually do this.
What I did:
- Movie #1 (mp4 version) is in the proper folder and Radarr sees it.
- Copied over an srt file to the directory that would belong to the movie.
- Go to Radarr->Movies>Manual Import
- a. Navigate to the directory that contains the replacement Movie #2 (mkv version)
- b. Select "Move Files" as the import mode.
- c. Click Import.
- Movie #2 (mkv version) is imported and shows up in Radarr. The srt file is still there.