Too little information has been given to help you with your process analyzer.
This automated GC can produce errors if the peaks have changed their retention times enough to be outside the integration windows, or if new analytes have reached the analytical column and are now interfering with the integration.
You should be talking to your vendor, sending them a chromatogram, or speaking to a senior engineer on your plant site with experience with your analyzer.
This is not the place to get help for YOUR GC and YOUR situation.
I have about 600 applications in the field that are using Applied Automation GC analyzers. Please, believe me and get the technical assistance you need from the proper source.
best wishes,
Rod