There is no way to do this right now, but I am supposed to implement this feature.
I do hope to have something working in a few weeks.
It would be very helpful if you could send me your Skyline document so I could see another example of how someone might want to use this upcoming feature.
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 that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
https://skyline.ms/files.url
-- Nick