MarkR s post is good info but may not apply here.
No - do not manually add or delete the 'cleared checkmark' - allow the reconcile function to do that.
What I thought you meant was the usual problem people run into - they successfully complete a reconciliation but later find an error in one of the reconciled postings that needs fixed. Changing a reconciled entry causes it to become 'uncleared' and throws out an existing reconciliation.
It is almost impossible to have 'cleared' too many items, but still end up with the correct closing balance - unless the 'excess' items were exactly offsetting If you used the wrong closing balance that also should have been (nearly) impossible to reconcile.
So if you 'cleared' items that were after the statement date - yet somehow still made it reconcile - then there must be other errors in that reconciliation If you 'plugged' the prior reconcilation to force an apparent balance and now want to fix it then delete the plug and then redo the reconcile as i described.