Yes, we should do something about the "View > Chromatograms" sub-menu when there are lots of replicates. When there are too many replicates, the regular menu items on there (Previous/Next Replicate and Close All Chromatograms) become too difficult to get to, so we should probably put the replicate menu items on a sub-sub-menu if there are too many of them.
I will try to fix this in an upcoming release of Skyline-Daily.
Skyline saves the state of all of your windows in a file with the extension ".sky.view".
I believe that if you do the following:
View > Chromatograms > Close All
File > Save
then it will properly save the state of all of the chromatogram windows being closed, and the next time you open the document they will still be closed.
By the way, we always like looking at Skyline documents that push the limits of what Skyline can handle. If it is convenient for you, it would be helpful if you could send us your Skyline document so that we can make sure that Skyline is not doing anything inefficient that does not scale well with the number of replicates.
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 and the .sky.view
If that .zip file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here: