just as a quick comment from my side without guarantee:
In our case we had files containing both SIM and Full Scan data. Skyline usually build chromatograms only for the SIMs from the raw files. To get chromatograms from the Full Scans we converted raw files to mzxml files using MS convert and additionally imported the mzxml files into the same or another skyline document. Might as well work with other file formats. Feel free to try it an write again if it does not work as described above.
Screenshot for freely available MS Convert and settings from a different post: