There is an old Trek novel called Cry of the Onlies that brought back Flint and did assert that Spock had repressed Kirk's memories of Rayna altogether, but as far as I can tell from the samples in Google Books, there's nothing there about the ship's databanks being altered. Which makes it rather less credible, since surely Kirk would review the mission logs afterward and would notice if they mentioned the existence of a woman he didn't remember encountering. Which supports the idea that Spock just made Kirk forget the depth of his feelings rather than her very existence.
I recently re-read that novel and you're correct that there was nothing mentioned about the logs being altered - plus McCoy still remembered the whole thing. When Kirk encountered Flint in the novel, he experienced feelings of anger towards Flint, but he didn't understand why since he didn't remember anything about Rayna at all. Flint, of course, still remembered the whole thing and was rather upset at Kirk since, not knowing what Spock had done, Flint thought that Kirk was "playing ignorant" about the whole thing. All of which forced Spock to come clean and explain to Kirk what he had done.