Here's what I would do:
1. Create a Skyline document which contains only unique peptides for each protein.
2. Create another Skyline document which contains the ten best peptides for each protein.
3. Export the list of proteins and peptides from these two documents into Excel and do something to figure out, for each protein, which are the unique peptides from the first document and which are the highest ranked peptides from the second document, and what would be the list of ten peptides that should be kept for each protein.
4. Merge your two Skyline documents together using the "File > Import > Document" menu item.
5. Use the "Refine > Accept Peptides" menu item to keep only the peptides that your Excel spreadsheet said to keep.
I am not sure exactly how to accomplish step 3. You might find the Custom Reports tutorial helpful in terms of exporting data to Excel:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports
-- Nick