Can you send us your Skyline document and a few of your raw files? We will figure out 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 your raw files are less than 50MB you can attach them to this support request. You can upload larger files here:
I cannot tell whether your data was SRM or chromatograms extracted from full spectra.
For SRM, the usual reason that chromatograms are "unavailable" is that there were not chromatograms in the raw file whose Q1 and Q3 values matched the precursor and transition m/z's in your document.
For full scan, the usual reason is that the MS/MS Acquisition settings at "Settings > Transition > Full Scan" did not result in MS2 spectra matching any of the precursors in your document.
We will probably be able to figure out what is going wrong after we see your files.