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Try this approach:
(project = FOO and issuetype not in ("Test", "Test Execution"))
(project = BAR and status != "In progress")
You get the idea?
Wrap a project key and the additional conditions in that project in parentheses, and connect them with OR. It is trivial.
Thanks Sushant, within each project I have to include more filters like issue type or states that are different in each project.
for example one query like this plus another one from another project
project = PV AND issuetype not in (Test, "Test Execution", "Test Plan", "Test Set", "Sub Test Execution")