When I unplug an email it still sits in flagged box

Likely you need to redo Spotlight index & then even wait a day or so.

How to rebuild the Spotlight index on your Mac

If searching your Mac doesn’t return expected results, rebuilding the Spotlight index might help.

1. Choose Apple menu () > System Preferences, then click Spotlight.
2. Click the Privacy tab.
3. Drag the folder or disk that you want to index again to the list of locations that Spotlight is prevented from searching. Or click the Add (+) button and select the folder or disk to add.
4. To add an item to the Privacy tab, you must have ownership permissions for that item. To learn about permissions, choose Help from the Finder menu bar, then search for “permissions.”
5. From the same list of locations, select the folder or disk that you just added. Then click the Remove (–) button to remove it from the list.
6. Quit System Preferences. Spotlight will reindex the contents of the folder or disk.