I have a Maule with some bubbling paint around several of the flap rivets. What is the communal wisdom regarding local repair versus fully stripping the flaps, re-chromating the whole surface and then re-painting? If a local repair is attempted, how much area around the bubbling paint should be removed before doing the local repair? Since the indications are around flap rivets, should the rivets be replaced even if the corrosion is found to be superficial when the paint is removed? What are the thoughts and recommendations of the collective wisdom here?

I dont know for sure but i would suspect that maule uses steel or steel stem rivets and you are seeing corrosion due to dissimilar corrosion. I know it is a very common sight on mauls or other airplanes with steel rivets on alum structure.
Obviously a full strip with a mix of grinding, sandblasting, rivet replacement and even re-skin would yield the nicest results. This would be over kill for most people and especially if you want to fly this summer. Maximum acceptable thickness loss of aluminum skin is usually 10%. Chromate anything primer is junk. If you are going to repaint use a good epoxy primer.

Spot blasters work well. They have a containment dome to keep the sand from going into your eyes and ears. Blast, etch alodine, prime, paint.
http://www.amazon.com/Aircraft-Tool-Supply-Rivet-Sandblaster/dp/B005VR84TG/ref=sr_1_6?ie=UTF8&qid=1405213147&sr=8-6&keywords=spot+blaster

You could use a die grinder with a scotch brite wheel.
You could drill out the rivet blast it, grind it and paint it replace the rivet.

With all that said unless you think the structure is being compromised or the rivet head is corroding off i would be inclined to leave it alone. Otherwise you are going to wind up with a million little spot paint repairs unless you chose to repaint the whole thing.

You could squirt some ACF-50 and that would stop the corrosion. It would be a little messy.

My previous owner did some local repairs. I'm more concerned about flying than appearance, so I'm ok with the fact that it looks a little wonky.

I have no idea why Maule used mismatched rivets for so long. Wonder if they still do.

As my long-time mechanic - AI used to say,
"Maule is the best homebuilt made in America."

CC

Flyhound, are you talking about the leading edge closure rivets on bottom of flaps, or wing skin dome rivets ? Big difference!