If I understand your situation, you found a duplicated entry, one was reconciled, one was not and you inadvertently deleted the reconciled transaction.
The solution should be to mark the remaining transaction as reconciled and then your beginning balance in the reconcile window should be correct.
In the end, the only thing that matters is that you only have one of the transactions and it is reconciled.
NOTE: Make a backup before doing any of these corrections so that if something goes badly wrong, you have a backup to restore to.