This question is in reference to Atlassian Documentation: Flagging an Issue
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To search for issues NOT flagged, you can simply negate the advanced search query, i.e. use either an explicit negation NOT
not (Flagged = Impediment)
or the shorthand notation for inequality
Flagged != Impediment
or, to be more future proof if more flag values get introduced, use NOT IN
Flagged not in (Impediment)
If you're looking for something that's not flagged at all, just negating it won't do the trick. You will want to check for Flagged being 'empty':
Flagged is EMPTY
For me, all these 3 variant gave an empty result.
This one has helped me (as in the other answer from Mike Drum):
This did not work for me: Flagged is EMPTY
It will still display FLAGGED issues.
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