One thing that might work would be to first tell Skyline about all of your modifications, and then tell Skyline to search your raw files using DIA Umpire.
Here is the Skyline DIA Umpire tutorial:
https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/DIA-Umpire-TTOF-20_2_1.pdf
It might be better if you looked at the latest version of that tutorial which is in this Word document:
https://github.com/ProteoWizard/pwiz/raw/master/pwiz_tools/Skyline/Documentation/Tutorials/Skyline%20DIA%20Umpire%20TTOF.docx

If you search your data using DIA Umpire, you would not tell Skyline which fragments to look for. Rather, after the raw files have been searched, Skyline would choose transitions based on what was actually seen.

By the way, if you have any questions about modifications in Skyline, I recommend this Webinar:
https://skyline.ms/webinar10.url

-- Nick