I've a short question so it should only require a short answer :-).
How does Rosetta numbering work with missing occupancies? For example, say we have a PDB structure containing three residues A6, A7, and A8. If all atoms of the second residue A7 have zero occupancy, does Rosetta map A6 to residue 1 and A8 to residue 2, omitting A7?
Yes, if enough atoms are missing for Rosetta to discard A7, residue A8 would get a pose numbering of 2. You can test this by passing a test structure through the scoring application with the -out:file:renumber_pdb option (along with the -output or -out:pdb options, respectively, for score or score_jd2), which should produce output pdbs renumbered according to pose numbering.
Note that you can force Rosetta to trust the coordinates for the zero occupancy atoms by including "-ignore_zero_occupancy false" (it's recently been renamed from "-trust_missing_coords true", which might be what it is in the version you're using).
Thanks for the answer (which I missed at the time). The scoring application tip is very useful.