Help needed: layers sometimes completely empty

There are two things that happen:

- A layer is completely empty because all of its elements ended up in another layer;
Like so:

- A layer is completely empty because all of its elements are still in the background.
Like so (you can see that the staff lines and text were extracted, but not the glyphs at all):

- (There was also one time where all three layers were completely empty because everything was in the background).

This phenomenon has happened at the beginning of iteration or later down the line, with cropped images or full images, with iteration or without. I'm making this issue because I'm not sure where to go from here and I want to make sure to have a record of it.

These models produce all empty layers (so no layer separation at all):
[Background Model MTWS 023 round 3.hdf5.zip](https://github.com/user-attachments/files/17012379/Background.Model.MTWS.023.round.3.hdf5.zip)
[Model 1 MTWS 023 round 3.hdf5.zip](https://github.com/user-attachments/files/17012492/Model.1.MTWS.023.round.3.hdf5.zip)
[Model 2 MTWS 023 round 3.hdf5.zip](https://github.com/user-attachments/files/17012502/Model.2.MTWS.023.round.3.hdf5.zip)
[Model 3 MTWS 023 round 3.hdf5.zip](https://github.com/user-attachments/files/17012524/Model.3.MTWS.023.round.3.hdf5.zip)

These models produce an empty layer 1:
[Beatrice 6+7 Background Model.hdf5.zip](https://github.com/user-attachments/files/17012390/Beatrice.6%2B7.Background.Model.hdf5.zip)
[Beatrice 6+7 Model 1.hdf5.zip](https://github.com/user-attachments/files/17012388/Beatrice.6%2B7.Model.1.hdf5.zip)
[Beatrice 6+7 Model 2.hdf5.zip](https://github.com/user-attachments/files/17012393/Beatrice.6%2B7.Model.2.hdf5.zip)
[Beatrice 6+7 Model 3.hdf5.zip](https://github.com/user-attachments/files/17012395/Beatrice.6%2B7.Model.3.hdf5.zip)

And these models produce empty layers 1 and 3 (so only layer 2 gets separated):
[Beatrice 7 part 2 Background Model.hdf5.zip](https://github.com/user-attachments/files/17012411/Beatrice.7.part.2.Background.Model.hdf5.zip)
[Beatrice 7 part 2 Model 1.hdf5.zip](https://github.com/user-attachments/files/17012416/Beatrice.7.part.2.Model.1.hdf5.zip)
[Beatrice 7 part 2 Model 2.hdf5.zip](https://github.com/user-attachments/files/17012423/Beatrice.7.part.2.Model.2.hdf5.zip)
[Beatrice 7 part 2 Model 3.hdf5.zip](https://github.com/user-attachments/files/17012429/Beatrice.7.part.2.Model.3.hdf5.zip)