How do I reconcile a bank account that has $60K in transactions deleted after the CPA reconciled it? They should stay deleted.

Reconciling means recognizing every transaction that cleared the bank account. If the CPA deleted 60K of transactions, they most likely never cleared the bank and since that's the case why were they in QBO? Do they belong to a different bank account or are they credit card transactions? If so, you need to add additional bank/CC accounts to your books. If not, then what were they, doubled transactions? Fake transactions? Paid by the owner personally? The point is, you can't reconcile transactions that didn't go through your business account.

Figure out where the 60K of transactions came from and take the next steps. 

Hope this helps. 

"How do I reconcile a bank account that has $60K in transactions deleted after the CPA reconciled it? They should stay deleted."

@tford 

It depends on why the transaction was deleted. It could be duplicated transaction or old uncleared transaction and so on. Hope it was not already cleared transaction that was deleted by mistake.

Normally, I would ignore the error message and reconcile for the same ending statement date again. If everything is ok, the difference should still be zero.