Someone else had the "Sequence contains no elements" error a few months ago:
https://skyline.ms/announcements/home/support/thread.view?rowId=64644

This seems to happen if you have some chromatograms with zero points in them.

I will try to fix this bug soon so that Skyline gracefully handles this scenario.

If you would like, you could send us your .wiff files and the .wiff.scan files that go with them. It might help me to come up with a better fix if I could see your data files. Also, it's conceivable that you might be running into a different error, in which case the fix that I am planning for the zero length chromatogram bug won't work.
Files which are less than 50MB can be attached to these support requests.
You can always upload larger files here:
https://skyline.ms/files.url
-- Nick

Note that this error only happens if you have set the "Explicit Retention Time" for any of the molecules which have an empty chromatogram.
If you set the "Explicit Retention Time" of all of your molecules to be blank then I believe you will be able to import chromatograms without error.

You can use the "Molecules" report in the Document Grid to set the explicit retention time values.

You can learn more about the Document Grid in the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

-- Nick