Here's how I think it went down:
Roy took a year off. His knees probably did feel a lot better. He probably was feeling noticeably better on a basketball court because A) he wasn't banging on his knees every day for the past year, and B) wasn't rehabbing from a surgery this time around.
Here's the thing, he's knees would probably be fine if he just wanted to go down to the local gym and shoot around a bit every few days, but that's NOTHING like the rigorous schedule that an NBA player puts his body through. I think Brandon wanted to believe that the prognosis wasn't as bad, and that his knees could hold up, but the doctors weren't lying to him. He doesn't have any meniscus in either knee. His knees can't play an NBA schedule, and he can't compete against the best players in the world anymore.
That's okay though, I think he needed to do this. He needed to know that he was done. He should be able to retire now knowing that he can no longer play the game of basketball. I also hope he calls his doctor friend on the Blazers staff and apologizes for doubting him.