This was due to the lack of upgrade pricing in the App Store; they essentially gave everyone the upgrade price for a while. $99 was always the intended "retail

This was due to the lack of upgrade pricing in the App Store; they essentially gave everyone the upgrade price for a while. $99 was always the intended "retail price"; now that they've abandoned the App Store, I expect Coda 3 will have separate pricing for upgrading vs. buying new.