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I keep in a database and work out programatically what has changed between versions and then manually decide which transactions to apply to the database to bring into sync (as much as I want to anyway) and at same time handle resultant splits/lumps of any affected sightings.
I've been using eBird which is based on the Cornell University list (James F Clements). They, too, are about to announce their annual update. Fortunately, the changes all happen automatically on eBird. The only change I've noticed in my list was that California clapper rail has become Ridgway's Rail - Rallus obsoletus. The 'split' hasn't affected my total list as I hadn't seen any other clapper rails.