OK, now I see the vimeo video. So the app crashes right after you open it. Unfortunately I still can't figure out how to reproduce the problem. And I also don't see a crashlog for this. Have you enabled sending analytical data to app developers in the iPad settings?
My suggestion to get rid of these crashes:
1) Create a backup in ST2
2) Delete all missing songs in ST2
3) Create another backup in ST2
4) Restore backup from step 1 in ST2
5) Restore backup from step 3 in ST3
Now for organizing your songs: Why not use playlists to group your songs? Or maybe the keyword feature. That way you only need 2 taps to display all songs with a certain keyword. And if you want to stick to your routine, recreate your dividers as placeholder songs. Then backup in ST3 and use this backup to get going should there be any new problems.