Hi there, @CASeller13.
I appreciate the in-depth information you shared in your post. This will help us narrow things down. Let me share a few information about making deposits in QuickBooks Online.
When you put money in the bank, you often deposit several payments together at once. The bank usually records these as a single deposit. You also need to group these payments together in QuickBooks so your records match.
If you wish to show the credits/refunds transactions when making a deposit, you'll need to make sure that the transactions are deposited to Undeposited Funds account. This way, all your sales or expense transactions under undeposited funds will show on your Bank Deposit page.
In addition, the Undeposited Funds account holds the records of invoices payments and sales receipts so you can group them together.
You might also want to read this article for more information:
Let me know in the comment section below if you have any other questions with QuickBooks Online. It'll be always my pleasure to lend a hand.