Glad to hear again from you, @qbo2.

I'd like an opportunity to clarify the reason why you're getting zero (0.00) in running your Profit ans Loss by Classes in QuickBooks Online.

If the bank deposit is created before creating the invoice, the deposit will be recorded under Unapplied Cash Payment Income. Just a heads-up though, deposit transactions should be recorded under the account "Account receivables" not on Unapplied cash Payment Income. 

So when you run the report for Accounts Receivable it will show an open balance  that you can apply to your invoice. On the other hand, when you run the Unapplied Cash Payment Income report it will show/report the invoice only.

Feel free to click on the Reply button if you have other questions about managing your transactions. I'm always here to help.