Thank you for your help. Your suggestion helped me figure out what had happened.
It finally dawned on me that the order of the detectors in the signals table determines the name of the signal (i.e. first row is FID1, second row is FID2, etc). When the GC was originally set up 10 years ago, the installer had put the rear detector in line 1 and the front detector in line 3 with diagnostics in the 2 and 4 lines. I don't know why but that was how it was set up. All our methods looked at FID3 for the front and FID1 for the back.
When I disconnected and reconnected the headspace unit, I had inadvertently changed the signals table so that I had the front FID on line one in the configuration. So it threw everything off. I fixed it and it seems to be working now.
Again, thanks for your help.