That depends. Does it look okay wet? That'll tell you if it's a pit from the top or a bubble underneath.
I would try carefully wet sanding the area with 600 grit paper. Make sure you don't break any edges. If the problem you have is pits, then you should be able to re-clear it and have it look decent (the clear will fill the pits).
If you have bubbles underneath, you might be hosed. If you're very lucky, you'll break through the top of the bubble when you sand and clear will fill inside them. That is unlikely, though.
If you break through the clear and disturb the basecoat you are hosed. You'll get a dark spot that won't go away without re-applying the clearcoat. I just did that trying to touch up a chip on the hood of my DGGM '94. Looks like some dipshit burned the clear... because some dipshit sanded through the clear.
My guess is you'll end up having to repaint the quarter, but it doesn't hurt to experiment. Color match on that car is a pain - there is enough pearl stuff in the MAB to make your life miserable. I would suggest a big blend area. Are you far enough from any edges with the bubbles that you can blend color towards the edges of the panel before clearing? If not, you will likely need to get the adjacent panels involved. Fortunately for our wagons the only adjacent panel that really matters is the rear door. You'll never notice a slight color mis-match on the D pillar or tailgate.