If you look under the details of the abuse filter, there's a tool to revert actions taken by this filter. If you click on that, you can select the time period for actions to be reverted. This should undo all of the listed actions, and give the user back their autoconfirmed status. Note that you cannot choose individual actions from the list; if you want to undo just one action, you need to make the time interval smaller.
I hope this helps. Let me know if you have any questions.