My guess is that Kirk handed the Enterprise over to Decker, he commanded the ship on various missions for a year, then brought it back to Earth to begin the refit.
Makes more sense than the the ship just sitting in orbit for a year, cooling it's heels.
It's possible that early work on Enterprise
's redesign took place during that year. If it had just been a standard refit, Enterprise
might have been out of drydock in a couple of months instead of a couple of years.
Shane Johnson's Mr. Scott's Guide to the Enterprise
had an interesting idea that Enterprise
's refit was originally meant to be a much simpler thing, but then snowballed into a total redesign of the existing vessel both inside and out. Similar things have happened in real life, so it's a plausible theory.