When I removed the handrails this summer while painting the deck, I caulked the holes and put a straight pin in each hole so I would find the hole after painting the deck. When I removed the handrails for varnishing (no deck painting), I covered each hole with duck tape.
For temporary seals I use a little blob of butyl in each hole. Roll it into a ball slightly larger than the hole and press around the edges to get a good seal.
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