Can you send us your Skyline document and one or more of your .raw files?
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files such as spectral libraries or extracted chromatograms.
You should also zip up one or more of your Waters raw file folders and send them to us too.
Files which are less than 50MB can be attached to this support request.
You can upload larger files here:
We have certainly had cases in the past where Skyline would spontaneously disappear because of a bug. What is supposed to happen is that the next time you start up Skyline, Skyline tells you that "Skyline had an unexpected error the last time you ran it." and ask you if you want to report the error. It sounds like that didn't happen for you, so the best thing for us to do is to try to reproduce this same bug on our computers.