when I mark as false positive a specific vulnerability (report->results->vulnerability->ignore), does it mark as false positive for all the web app or only for the one I put on ignore?
Should only be for that Application.
Qualys documentation should be clear on this but you can test.
Create a copy of your application and scan both App1 and the copy. Then make the vulnerability in App1 as false and try to report on both. You should not see it in App1 and you should see it in the copy.
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