This requires knowing what files are processed and in what order.
The main input file for NRLMOL is SYMBOL, so it will start from there. This file is processed first even if there is a CLUSTER file present, so if you make changes to your CLUSTER geometry file then don't forget to remove the SYMBOL file to force NRLMOL to read the new geometry. When NRLMOL verifies that there is no SYMBOL file, it reads the CLUSTER file to create a new SYMBOL and ISYMGEN files: the first contains the geometry and the second the basis set information. These two files are later merged into a single file called INPUT, which contains both geometry and basis set information.
However, if you do not have the ISYMGEN file, but instead have the INPUT file, then do not start from SYMBOL. What you can do is start from the CLUSTER file along with the INPUT file. NRLMOL will read the CLUSTER file and create a new SYMBOL file from it; the program will read the basis information from the INPUT file and will create an empty ISYMGEN file.