Can you send us your Skyline document as well as your .wiff or .wiff2 files and the .wiff.scan files that go with them?
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files.
The Share Document dialog also gives you the option to include the .wiff files in the .zip, or you can package them up and send them separately.
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