Sadly, it's painfully simple to mess up the paperwork, and the FAA/Boeing systems make it more so.
Even after a change is certified, there is a requirement to notify the FAA of it's first installation in each major and minor model - so for example it you certify the change for the 737NG, you'd need to notify of the first time it was delivered in a 737-700, 737-800, 737-900, and if they ever built another the 737-600.
When we put together the cert plans, we need to call out the incorporation point for each minor model. However, that's months (or even years) before the actual incorporation, schedules change, and new aircraft don't always deliver in line number order, so it's really easy to mess this part up - and the Boeing system doesn't help.
I personally got caught up in this shortly before I retired on the 747-8 - we'd made an engine control change, did everything per the cert plan, with incorporation points for both the 747-8 and the 747-8F. Except that the airline that was supposed to receive the first 747-8 went bankrupt and the aircraft 'ticket' and delivery didn't happen, but no one bothered to inform me. We delivered half a dozen 747-8 Intercontinentals with the change before we stumbled across the issue and informed the FAA - they were not amused. I spent the next month arguing with the Boeing Regulatory Administration (RA) over who was responsible - me or the RA. I finally threw it back and them and said they needed a system that - if a delivery was delayed or cancelled - would notify the Cert Plan owners who called out that aircraft as initial incorporation so they could take appropriate action. Since such a system was not in place, it was the RA's fault and they owned the escape. They didn't figure out how to throw it back at me before I retired - no idea what happened after that...