If I’m reading your question correctly, you’re trying to detect differences between a physical file created from a spool file against another physical file created from another spool file?
the command, CMPPFM (Compare Physical File Member) does just that. I’ve not used the command in a CL, but I’ve used it many times from the command line to detect differences (or confirm sameness). One thing to watch for:
If your reports contain a run-time or date in the headings, those will likely be detected as differences, so you might want to strip out the records that contain those elements before running the compare.
Hope this helps.