Hi Alejandro,
I just tried phenix.maps, and it yields substantially different difference maps than those obtained through my refinement process.
not surprising at all because phenix.refine changes the model and phenix.maps uses input model as is to compute maps!
Are there any other techniques or parameters I can modify to make residues with multiple conformations 'invisible' to phenix.refine, in addition/besides set occupancies to 0 or deleting the residue form the pdb file?
No. They will be always visible to geometry restraints.
Pavel