Can you post a screenshot just so I am sure? Are you referring to the "Only integrate significant q values" option in the "Reintegrate" form? You are setting the "Q value cutoff" to 0.01? (or 1% FDR)
That is a peak-level (or query level) cutoff, with the impact that if the peak-level (i.e. peptidoform, chromatogram peak group) q value is greater than 0.01, then the peak is not integrated and all peak statistics are given #N/A values.
There is no setting I know of in Skyline that would allow you to disallow integration based on the run-count where detections occurred, but there may be in the next version of Skyline. We are working on adding both peptide-level and protein-level q values which can be used to exclude results where a peptide or protein is not detected below a certain q value cut-off (or corresponding FDR) even though some of its peaks may still have a low enough peak-level q value (which makes those peak detections more likely false-positives). See the following paper for a discussion of these concepts:
Once we have these added q value types, we intend to also add a new "Detection" tab to the Refine > Advanced form, which will also contain filters for peak-level detection by number of runs, as you seem to be suggesting.
Not there yet, though. If I have misunderstood what you are doing or asking for, please reply with new details.