Can you send us your Waters .raw folders, or does this problem only happen when you are telling Skyline to extract chromatograms from a Unifi server?
If possible, could you zip up one or more of your .raw file folders and send them to us? Files which are less than 50MB can be attached to this support request. You can upload larger files here:
It would also be helpful if you could send us your Skyline document. In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
If you cannot send us your Waters .raw folders, then it might be possible for you to get more information about the error that caused Skyline to abruptly exit.
Sometimes when Skyline abruptly exits, the next time that you start up Skyline, Skyline will show you the "Unexpected Shutdown" dialog and allow you to report the error to us. Did you happen to see a dialog like that?
Other times when Skyline abruptly exits there is additional error information available in the Windows Event Viewer.
Here is a page with helpful information about how to use the Windows Event Viewer:
You might also get useful information if you use ProteoWizard MSConvert to try to convert your Waters data to .mzML.
You can install MSConvert from here:
The way that MSConvert reads data from a Unifi server is similar to the way that Skyline does it, so it would be helpful if we knew whether MSConvert had the same behavior.