Neumes from two staves grouped in one staff - other staff absent

Quite often, one staff on the folio is completely absent and its neumes are all on the staff above. Two distinct phenomenons seem possible here:
1. The two staves are actually present one on top of the other and all the neumes are assigned to the correct staff. This issue is easily fixed, because one can just select the entire staff and move it to its correct place. This phenomenon is much rarer than the other;
2. There is only one staff, and all the neumes are assigned to that staff. This problem can be fixed by creating the missing staff, then individually moving each neume to its correct place on that new staff, then reassigning them to the nearest staff. This phenomenon is what usually happens.

Some illustrations:
Folio 054v is fun, because it shows both; with the staves highlighted, you can see that the example on the top has both staves separate, whereas the example on the bottom has all the neumes associated to the one staff:

Another example of phenomenon 2 is in folio 078r; in this case, the neumes from the third staff from the bottom actually "leapt" over a whole paragraph of text to merge with the orange staff:

The MEI files:
[Rodan-generated Manifest_054v_initially_1 staff mixed and 1 neumes mixed.mei.zip](https://github.com/DDMAL/MEI_encoding/files/6561507/Rodan-generated.Manifest_054v_initially_1.staff.mixed.and.1.neumes.mixed.mei.zip)
[Neumes on staff above 078r.zip](https://github.com/DDMAL/MEI_encoding/files/6561508/Neumes.on.staff.above.078r.zip)