I am not sure whether you can trust anything about a peak scoring model that has been trained on second best peaks.
I gave a bit of an explanation for that here:
https://skyline.ms/announcements/home/support/thread.view?rowId=51479
If you send us your data we might be able to come up with better advice.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files.
The Share Document dialog gives you the option to include the mass spec data files or you could send them to us separately.
Files which are less than 50MB can be attached to these support request.
For larger files, you can always zip everything up and upload them here:
https://skyline.ms/files.url
-- Nick