I have the same problem.  I have contacted support, spent hours on the phone, and submitted feedback.  I could never even get someone to acknowledge that it was a bug.  Having Quickbooks generate an invoice number is a very simple thing.  Why have a setting to turn off custom numbers if that setting gets changed when you open an invoice in Quickbooks online?  The new invoice format has broken my integration.  It is very easy to reproduce this bug.  Please fix it.