I am not sure why your chromatograms look the way that they do.
Can you send me your raw files "20210729_AH_Leela_LQE_PRTC_00_TC20210729_KY.raw" and "20210911_MH_LQE_PRTC_MH_SN20138917_1.raw"?
I see that at:
Settings > Transition Settings > Full Scan
you have "Retention Time Filtering" set to "Use only scans within 30 minutes of MS/MS IDs".
That setting would certainly limit the length of chromatograms that were extracted to be about 60 minutes long, or longer if the MS/MS ids were far apart from each other (the extraction range extends 30 minutes from the first matching MS/MS ID to 30 minutes after the last MS/MS ID).
The chromatograms in your Skyline document are much shorter than 60 minutes. Was that Retention Time Filtering setting maybe different when you told Skyline to import results? If you make a change to a setting that affects chromatogram extraction, you should tell Skyline to extract the chromatograms again so that you can see the effect of that change. Typically you do that using:
Edit > Manage Results > Reimport
Can you provide the settings required to view the entire chromatogram range?
In the files that I sent, when I import the first raw file, the entire range is shown. However, when I import the second file "MH...", a shorted range is shown. It makes me think that there is something different or wrong with the second raw file.