Because we continued writing 100% of the data to Mongo until we were certain that everything was working, it was always safe to stop using Dynamo (or use it for less traffic). In the canary read phase, we always returned the mongo data to the caller. We read from both sources, compared the data, logged an error if there was a difference, and discarded the dynamo data.
In this way, the Dynamo data was kind of throw-away, until we were confident in everything.
The new DB is not authoritative until the final step of the switchover, so you could easily scrap it at any point.