Hello cornerstonemgmtg,

You get this error when trying to make some changes on a reconciled bank account. It'll definitely adjust the balance and create discrepancy. 

This is how you should receive and match the deposits.

1. Create an invoice.
2. Receive payment  and choose Undeposited Funds in the Deposit to field. 
3. Make a deposit by clicking on the Plus icon and then Bank Deposit.
4. Select the invoice payment.
5. Once the deposit is downloaded in the Banking page, system will match it to the deposit you've created in step 4.
6. You click on the Match button to reconcile it. 

You can correct the reconciled bank account by undoing the transactions. Please check out this article for more information: How To Unreconcile A Transaction or Undo A Reconciliation. Creating journal entries won't fix the undeposited transactions. You'll need to clear them first. 

You may also want to ask for more help from your accountant on how for a few pieces of advice. 

If you need anything else, please let us know.