Such great pains come with huge systems. What's the alternative?
Taking the platform offline for a few hours? Management will say no. Or maybe Management will say yes once every three years, severely limiting your ability to refactor.
Doing a quick copy, and hope nobody complains about inconsistencies? Their reputation would suffer severely.
From the article I got the impression that both tables were being written to in the same database transaction, so this is not a possible failure scenario at all.
I'd like to hear about alternatives if you've had experience.
In the past I have either flagged records to say where the system should read the data from, or just built logic into the readers to say if there is no data in A, read from B.
Then you update the writers to migrate the data from A to B on every new update and remove the data from A. It is an expensive 1 time write to move the data, but then you don't have to worry about keeping data in sync across two storage locations.
What you end up with is all records that are actively getting worked on move first. At a later date you start migrating all those stale records from A to B with a background process. Once A is empty, remove the logic to read from A, remove the migration writes, remove the A datasource.