After you file

Yes your post doesn't make sense.  I don't think the IRS would charge you bank account for 5600 for either the original return or the amended.  When did they take it?   Are you sure you are not just seeing the deposit for the 3rd Stimulus payment?  

And you should not have amended for that.  The IRS will automatically adjust your return if you had the wrong amount on line 30 for the Recovery Rebate Credit (3rd Stimulus payment) and send you a bill.  I assume you had 5600 on line 30?