You can't search the history with the default JQL (except by using was and changed).
In Jira, you can see the history of flags on the single issue level while opening the Activity section.
I can also suggest checking Issue History for Jira app where you can get a report for some project, sprint, or dates (filtering the items you need).
If you add the flagged field to the grid's columns, you'll see flag changes for the list of issues.
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