You should be able to find the peaks that have been integrated by "alignment" only of IDs in other runs, i.e. no IDs for either label type, by using the Precursor Results.Identified column in a report. The values should be "TRUE", "FALSE", "ALIGNED". It sounds like you want only ALIGNED. Would just having this column in a report be enough for you to calculate your statistics, or do you truly need to remove the peak integration for these peaks so that Skyline would use #N/A for all of the peak statistics?
So far, we don't have an easy way to remove peaks in the Document Grid. So, you would need to use linked columns in the document grid to navigate to the peaks and then right-click > Remove Peak, which is probably prohibitively manual.
I just spoke with Nick, and he said he would think about a way to allow you to remove peaks for any set of PrecursorResults you can select in the Document Grid.
Sorry, we don't have a better answer for you at the moment.