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.
Ah, okay. Yes, I got the same results as you, even if you do it the opposite way, add a movie through Radarr, and it will replace the other movie and wipe the other data.
Through my testing, it does seem to only wipe it if Radarr thinks there's a movie there already. I don't think this solves your problem, but if you empty the movie folder, scan and refresh radarr, then add the data back, it gets picked up. It only wipes the data when it is replacing it, which is probably intentional because different files might have different metadata? I'm not sure.
It might be possible with a custom script.
Before that, take a look at the "Import Extra Files" option under Settings -> Media Management.