Regarding the version 2 problem see here: https://support.stagetraxx.com/d/600-caution-updating-to-ios145-with-version-2-of-stage-traxx
Did switch AppleIDs after buying version 2? As far as I can tell that's the main reason for this problem.
There is no "Repair link" function in version 3 because all audio files are copied into the app and can't go missing. Except when you delete a song, it will also remove the audio file. If you had another song that pointed to the same audio file, that one will go missing. Or if you delete an audio file in the Files app from the Stage Traxx 3 folder, it will then also be missing in the app. So please explain in detail when a song gets missing.
When you open song details for a missing song, you can see which audio file it tries to load. Make sure that this file is available in the Stage Traxx 3 folder. This will effectively repair the song.