Can you send us your Skyline document and .raw file?
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 your .raw file are less than 50MB you can attach them to this support request.
You can upload larger files here:
I am thinking that the behavior your are seeing might have something to do with the way that Skyline tries to extract one for "SIM" spectra, and a separate chromatogram for regular MS1 spectra. The way that Skyline decides that a spectrum is "SIM" spectrum is Skyline looks at the width of the m/z window that was scanned. If the width of that window is less than 500 Daltons, then it goes in the "SIM" chromatogram instead of the regular MS1 chromatogram. (It used to be that the 500 Dalton cutoff was a much smaller number, but for various reasons we have increased that number over the years.) If the SIM chromatogram has any points in it, then that is what Skyline ends up using instead of the MS1 chromatogram.
In Skyline-Daily there is a checkbox "Ignore SIM scans" on the "Settings > Transition Settings > Full Scan" dialog. It might be that checking that checkbox will fix your problem, or it might be that checking that checkbox will just result in your chromatogram looking like the missing half what you have in the screenshot.
It is likely that the behavior your are seeing has nothing to do with Skyline's SIM spectrum behavior. I cannot think of a reason that the chromatogram would suddenly jump down to zero the way that it does in your screenshot.
After we see the files that you send us we will probably be able to figure out what is going wrong.