How can I reconcile my checking account when i have a deposit that was deleted intentionally, due to an error, but the beginning balance is now messed up?

I'll help you with reconciling the bank account, Bruce-derouen.

When you deleted the deposit, it caused the beginning balance to be off. Since it was intentionally deleted, so this means that the transaction is not part of the previous reconciliation. Having said that, we'll have to unreconcile and reconcile the previous period again. This way, QuickBooks Online will recognize the accurate and new balance. 

When you undo a reconciliation, you'll have to edit each transaction. Here's how:

1. Click Accounting, then go to the Chart of Accounts tab.
2. Select the bank account, then click View register.
3. Select the transaction you want to unreconcile.
4. Select the box where you can see R, then continue clicking until it's blank.
5. Click Save. 

Once done, reconcile the bank account again. The beginning balance on the current period should be correct by then. 

If you have additional questions, please feel free to get back to this thread.