Normally you can just supply a symmetry file with N operators produced by Phenix (ends in .ncs_spec) and a model with one chain to ApplyNCS and it should create a new model with N copies of your chain.
The output model may indeed be missing the header information. You can copy that from your original model if you like.
As this did not work for you, can you possibly try this example which I have just tested:
in the Phenix GUI, go to "New Project", and select "Set up Tutorial Data". Then scroll down and choose "Docking and Refinement" of GroEL and hit ok to set up tutorial data.
1.Superpose 1ss8_A.pdb on chain A of 5w0s.pdb
Under "Models: superpose, search...", select sequence-based superposition.
Enter a title like "Superpose 1ss8_A.pdb on chain A of 5w0s.pdb"
Load the 5w0s.pdb as your fixed model
Load the 1ss8_A.pdb model as your moving model
Enter 1ss8_A_superposed.pdb as your output model
Add "ChainA" under selection for fixed model
Hit Run to superpose 1ss8_A.pdb on chain A of 5w0s.pdb
2. Get NCS operators from 5w0s.pdb
Under Models: superpose, search...", select "Find NCS operators"
Enter at title like "Get NCS operators from 5w0s.pdb"
For PDB file, select 5w0s.pdb
Hit run to get your NCS operators.
3. Apply the NCS operators from 5w0s.pdb to 1ss8_A_superposed.pdb
The FindNCS GUI will put up a button called "Apply NCS operators". Hit that button and a FindNCS window appears with the symmetry file filled in. You can also open FindNCS directly and select your "groel_dock_refine/FindNCS_2/find_ncs_2.ncs_spec" or similar file.
Enter 1ss8_A_superposed.pdb as your input pdb file and hit Run.
Hit Open in Coot to show your expanded PDB file. You can also load in 5w0s.pdb and see that they are similar.
If that does not work, please let us know! If it does, then you can follow the same steps for your case. If your case does not work, it would be great if you can send in a bug report and attach your files so that we can reproduce the result, and we will fix it!
I hope that helps!
All the best,
Tom T