I think the underlying problem is that Phenix ADDS on PDB files defined at the commandline to whatever is defined in the .def file. I mentioned this a couple of year back to Ralf as an improvement request, but did not get very far. If one could force Phenix only to only read the pdb file defined on the command line and ignore the one in the *002.def file these kind of minor headaches would go away.
It is tricky to support both input of multiple pdb files and easily overriding the pdb file name in the .def file. Maybe I've made the wrong choice when deciding which of the two features is more important? How often do people want to give multiple pdb files to phenix.refine? If that's less common than the wish to override the name in the .def file we could change phenix.refine to only allow one file name. It would only use the last one given (like any other non-multiple parameter). Multiple pdb files would then need to be concatenated externally. It would be an easy change. Ralf