If these are spells unique to SkyRe & Requiem, you will have to load those files as masters in order for the plugin to work correctly. This ensures that they get listed as masters in your new plugin.
The easiest way to do this is to use WryeBash. Boot up WryeBash, and then right click on Skyre_Main.esp and choose "Esmify self"
This sets the esm flag on the file, so that the C.K. will think it is a master file.
Now boot up the C.K., selecting Skyre_main.esp - and don't set anything as the active file.
Once it loads, make your changes and save a new plugin. Your new plugin will have Skyre_main.esp as its master file, and it will now work correctly.
Dont forget to go back to WryeBash and right click the SkyRe file, this time choosing "Espify self" to turn it back into an esp.
Rinse & repeat for Requiem.
I don't think you can fix both in one patch file if that is what you were attempting, I think they will need to be separate patches so that only one or the other is required as a master for users.