This isn't exactly the same thing, but I think the principle still applies.
Years ago I re-caulked the hull of a wooden boat and worked hard to get the polysuphide that I topped the joints with dead flush. When the planks expanded, the caulk sat higher than the planks, just as you describe with your deck. I shaved off that high spot using a very sharp chisel; just carefully pushed it along trimming the caulk flush with the planks. Sometimes it would dig in when I wasn't careful enough, but those instances were easily sanded out.
HOWEVER...... If I'm not mistaken, the caulk joint on decking doesn't go the full thickness of the plank. If the deck is worn down and you remove the caulk, you might expose the joint.