What a timely question!  I am in the process of doing exactly that. I have an impact wrench with a flat blade screwdriver bit that has been the only way most of these bolts come out.  It is VITAL that the bit fit the screws very closely.

When we bought Harmonie we were told that pulling these screws and re-seating them after treating with Tef-Gel should be a once in ten-year project on any Amel.  If it is done often it is easy.  If not... it is a miserable project.

Rust at the base of the stanchions can come from three sources.

On Harmonie there is no bedding compound between the flat part of the stanchion base and the fiberglass gunwale.  This means that there is a fairly large flat area of stainless steel that is mostly excluded from the oxygen in the air that protects it from corrosion, but where water can creep in and get rust started.  This is the least critical rust issue. I see it on each of the stanchions I have removed so far, even on those that showed no visible rust stains around them before removal.

The bolts themselves can corrode on the underside of the head.  Again, a place where water can get to, but has limited access to air.  The problem with this is it can significantly weaken the bolt.  I have seen stainless bolts with this kind of corrosion where the head literally fell off.  So far I have found one bolt like this.  The head twisted off when I put torque on it to remove.  I am in the process now of drilling it out for removal. Not my idea of fun.

The last possible source of rust staining is the most serious, and is the real reason for making this a routine maintenance project.  When water finds its way down into the threads of the bolts it begins to corrode the steel plate that Amel set into the fiberglass. The resulting rust irresistibly expands and will destroy the fiberglass around it in a very slow motion explosion. This requires a complex, and expensive repair.

The impact wrench has been successful at removing the bolts so far (except the one that broke!)  After removal the heads are beat up enough that I am replacing them with the most corrosion resistant machine screws I can find--of 316L stainless. 

The rail has a joint about a meter forward of the aft corner.  Once you get the rear two stanchions unbolted, that piece can be removed. (The stanchion all the way back on the transom is through bolted, not in a tapped hole.)

Once you get a few stanchions unbolted, you will have enough "wiggle room" to lift each of the stanchion bases up, clean them up, and get some caulking under them.  Since the stainless screws are going to be threaded into steel backing plates, they should be generously treated with Tef-Gel or whatever  brand of anti-corrosion thread lubricant is your favorite.  Then all will be better for another decade!