If you are using Apple Mail...
Open Mail
Click on the "Flagged" option. It is to the right of the "Sent" option.
Once you have clicked the "Flagged" option, Command+A. This will highlight all the flagged emails.
Next, right click on the highlighted flagged emails. You should see an x (which is the clear flags) option. Click it, and it will remove the flags from the emails.