I am not sure I understand what sort of data you have.
Are these MS1 chromatograms extracted from spectra? Are you saying that these extracted chromatograms should be longer than they are, but Skyline is truncating them?
One of the reasons that Skyline might truncate your chromatograms is because of what you selected at:
Settings > Transition Settings > Filter > Retention Time Filtering
and you can fix this by choosing "include all matching scans".
Another reason that Skyline may truncate your chromatograms is if you have MS1 and MS2 transitions in your document for the same molecule. If Skyline sees that the extracted MS2 chromatograms are shorter than the MS1 chromatograms for the same molecule, then Skyline will truncate the MS1 chromatograms to match the MS2 chromatograms. The confusing thing is that Skyline will do this even if the MS1 and MS2 transitions are in completely different places in the document, but the molecules that the two set of transitions belong to have the same Molecule Name. The workaround for this would be to change the name of the molecule with the MS2 transitions to something else like "ADMA_ms2".
If you would like, you can send us your Skyline document and a few of your raw files and we can see what is going on.
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 and those raw files are less than 50MB you can attach them to this support request.
Otherwise, you can upload them here: