I've tried `Set Field Value to constant or Groovy expression` function and setting Raw value to empty value. It doesn't remove the flag.
Try the free addon JIRA suite utilities and the clear field value post-function:
https://marketplace.atlassian.com/plugins/com.googlecode.jira-suite-utilities/server/overview
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Opps, sorry - it's been so long that I forgot it's a plugin - Christian's right; install the plugin, then you can do what I outlined.
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