If you have RAPs on 3.x and you have a spare controller, I would put the spare on 5.0.4.2 and upgrade your RAP backup partitions from that controller then provision over to your 6.x controller.
Downgrading your production 6.x controller to 5.x to upgrade some older RAPs should be done with care. You can potentially lose some configuration components when downgrading and they won't be there when you upgrade again. Not to mention that you'll take down your entire RAP network just to upgrade some old RAPs.