payment received and deposited in wrong company

I'd be glad to help you correct the payment and the A/R report as well, W012.

I'd also like to ask if these two business has its own company file? I can think of two options on how to remove the transaction in your A/R account. 

First, you can delete the payment that's incorrectly recorded. Here's how:

1. Go to the Customer Center and proceed to the Transactions tab.
2. Select Received Payments.
3. Look for the payment and double-click on it.
4. Click the Delete button and select OK.

Check out this article for more details: Resolve Common Issues When Applying a Payment Towards an Invoice.

If the transaction was actually deposited and downloaded in the second company, you can change the account used from A/R to a different one. However, I would strongly recommend reaching out to your accountant for further advice on this matter. 

Let me add a couple more articles for additional references: 

• Add and Match Bank Feed Transactions in QuickBooks Desktop
• Customize Customer, Job, and Sales Reports in QuickBooks Desktop 

Don't hesitate to reply to me or ask more questions if you still need more help. I'll jump right back to help you again.

Thank you JenoP for your suggestion. Yes, we do have 2 separate QB company files; however the checks were actually deposited into the bank initially (the bank for the Retail biz); so we cannot just delete the transaction because that throws off our bank reconciliation. The funds were deposited in December to Retail, and then moved when the error was discovered in January; we moved the funds from retail's bank to B2B's bank by writing a check.

After thinking about this more, I realize that... in QB's deposit transaction... we recorded the "from account"  as  "Accounts Receivable", but since this was not a true accounts receivable due for the Retail biz, I believe the right thing is to change this field in the transaction to "Other Income".  Does this sound right"?