If you withdraw an excess contribution before the extended due date, then you will need to withdraw the excess contribution plus earnings and it will be treated as never contributed, therefore you can avoid the 6% penalty. Please see Withdrawal of excess contributions for details.
If you withdraw the excess contribution after the extended due date, then you will have to pay the 6% penalty but you can leave the earnings in the account and therefore will request a regular distribution in the amount of the excess contribution.
@gjgogol
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