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Hi @533076076,
Yes, the newly added bill payment will affect your reconciliation where you need to make some adjustments. And I'd be glad to guide you on how to get this done.
First off, let's un-reconcile the register that includes the period where the bill payment belongs.
Then, you can proceed to re-reconciling your register and make sure to include the newly added bill payment. You can read this article to learn more about this process: Undo and remove transactions from reconciliations in QuickBooks Online.
For your second concern, your customer will receive a payment receipt when you choose Save and send at the bottom right of the Receive Payment page (when recording an invoice payment). I added a screenshot below for your reference.
Also, I'm thinking that this another article may come in handy to you while dealing with your year-end tasks and filings: Year-end guide and checklist.
Let me know in the Comments section below if you need any other help. I'll be here to lend a hand.
Thank you
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