I think there's some misconceptions going around about how exactly NeoLemmix picks a music file, and how the fallback-if-not-found works.
Let me clear up exactly what happens (or at least what should be happening; any deviation from this is a bug).
Once a suitable file is found, use it, do not look any further.
When multiple musics with the right filename exist in the same place, but with different extensions, the order of priority (highest to lowest) is: OGG, WAV, AIFF, AIF, MP3, MO3, IT, MOD, XM, S3M, MTM, UMX.
1. If the level specifies a music file, look for that specific track.
>> Check in the game-specific music pack for that track, if there is one
>> Check in the "music" folder
>> Check in the NXP
>> Check in NeoLemmix.exe
2. If the level doesn't specify a music file, or if it did but the music file cannot be found; use the general rotation specified for the current pack (or if it's a single level, pick a random track from the Orig and OhNo tracks).
>> Check in the same order as in step 1
3. If the appropriate track based on the rotation can't be found either, do not play music.
There is no intermediate step of "If the track according to the pack's specified rotation isn't found, use the track according to the default rotation."
Therefore, it is quite simple to find out which track is missing:
- If the level does not specify a music, and the result is silence, the missing track is whatever the pack in question's rotation should play at this point.
- If the level does specify a music, and the result is a track based on the rotation, the missing track is the specified one.
- If the levle does specify a music, and the result is silence, both the specified music and the track that should play from the rotation are missing.
Additionally, the Issue Checker in the Flexi Toolkit should detect these problems.
In regards to changing back to the old behaviour, or adding a config option, I don't see this as very worthwhile - indeed, the removal of the warning was quite strongly requested.
