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For the Prestige Class, I'm not sure, but the feats are clear: You can use Magic Gear to qualify for feats, but you can't use the feat if you somehow lose the gear that gives you the requirements.
For the prestige class... that could be even worse, losing whole levels because you lost your +2 Dex ioun stone, frankly. So I would rule that as a "no" for the player's sake (not to mention my own, since I would feel compelled to not try to take that piece of gear from the PC).
Also, please do note that you need to wear the item for 24 hours before the bonus being considered "permanent".