Please tell your engineers that they may be able to reproduce the bug by doing the following:

• Make a copy of an invoice that was created as a recurring invoice for Customer A, say, for every Friday.
• Future date this invoice to next Friday, and change the customer name on the invoice to a customer that doesn't have any recurring invoices- Customer B.
• Save and close the invoice. It should ask you if you want to update the template for recurring invoices, or save this invoice 'just this once'-- click just once.
• Now, whenever you make edits to this transaction, QB will ask if you want to update the transaction for all recurring transactions or just once (Customer B doesn't actually have any recurring invoices, but its invoice is based off of Customer A's recurring invoice).
• I think at this point there may be confusion in your model about whether the new invoice for Customer B counts as the recurring invoice for Customer A or not.
• Chaos ensues.

This is my guess based on noticing the circumstances under which I run into problems with recurring invoices not running - there is always a one-off future-dated invoice set to run on the same day as the recurring transactions.