Your confusion ends here, @Jemma14.

Yes. Any recorded transactions in QuickBooks can adjust your reconciliation balance. If the bill pay transaction can cause a discrepancy in your balance, I recommend seeking help from your accountant for more guidance.

You might want to read this article to learn how adjusted reconciliations affect your books: Learn the reconcile workflow in QuickBooks.

Please let me know if you need clarification about this, or there's anything else I can do for you. I'll be standing by for your response, @Jemma14.