It sounds like Skyline might actually have discarded the chromatogram data outside of the range that you are seeing.
There are a few reasons that Skyline might discard that data:
There is a setting "Retention Time Filtering" at "Settings > Transition Settings > Full Scan" which can tell Skyline to only keep the part of the chromatogram within a certain time range.
Also, if you are collecting both MS2 and MS1 data, and Skyline sees that the MS2 chromatogram covers a smaller range than the MS1 chromatogram, the MS1 chromatogram will be truncated to match the MS2 data that exists. Skyline does this because it is the correct thing to do for scheduled PRM.
One scenario where this is the wrong thing for Skyline to be doing is for DDA data. If this was DDA data, you should be sure to choose "DDA" as the MS/MS filtering Acquisition method at "Settings > Transition Settings > Full Scan".
You should also check to make sure that you have not typed any numbers in for "Min time" or "Max time" at "Settings > Transition Settings > Instrument", because that will limit the length of chromatograms that Skyline extracts.
If you would like, you can send us your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
If that .zip file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here:
It might also be helpful if we could see a screenshot of what you are seeing.