The problem happens when a user makes the parent customer a subcustomer of another, after the payment was created. This then creates a three-level customer hierarchy. The top-level customer who received the payment for the child customers is now a mid-level customer. Please take note, that if the Consolidated Payments feature is enabled, it allows user to accept payments either through top-level customers or individual subcustomers only, but not through mid-level customers (Enhancement 245714).
The solution here is to edit the mid-level customer record and unset the value in the Parent field. This will make this customer a top-level customer again, allowing it to see all invoices from the child customers again.