I have done some lab scale H2S analysis, and have learned that there are many difficulties around analyzing for H2S with a standard GC. You don't give any details of the system -- Is the H2S analyzer completely separate, or is it a special detector added to the chromatography system -- but my generic answer is that it was deemed necessary to use a separate H2S analyzer in order to get a good analysis of the H2S in the pipeline.
I would suggest that you consult with a good analytical chemist who is familiar with the different methods for analyzing your gas composition, including H2S. Such a chemist should be able to explain in more detail why someone may choose not to rely solely on chromatography for the H2S analysis. In my limited understanding, it is simply that chromatography (at least -- traditional GC-FID, GC-TCD type chromatographs) is often not considered to be sufficiently reliable for H2S analysis.