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:
https://skyline.ms/files.url

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.
-- Nick

HI Nick,

The Skyline document and some raw files should be uploaded. I did get a few files to load, but the others have been consistently causing a crash. I haven't seen any errors upon restart. Thanks for your help.

Thank you for sending those files.
Yes, I have no trouble reproducing this error on my machine.
I will try to find someone who can fix this.
-- Nick

Thank you, let me know if you need anything else from me.