QB Issue Resolution:

Splitting the entry from the bank feed may not have attached the outstanding invoices. There is no need to split the payment but instead, “Receive Payment”, select the two invoices, save as a deposit alone or posted to Undeposited Funds to be included with other receipts.

Resolution for Issue 'I am reconciling my bank account, which shows a payment from a customer which covers 2 invoices. I split the entry but QB hasn’t shown those invoices as paid?' available: Yes (Solved).
Source: Intuit Community forum.

I am reconciling my bank account, which shows a payment from a customer which covers 2 invoices. I split the entry but QB hasn’t shown those invoices as paid?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for Invoices
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Error Recovery for Invoices [Canada]
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