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Refractometers become less accurate once the yeast has started fermenting the sugars into alcohol. It fails to take into account that there is sugar, alcohol, and water in solution, and only measures the sugar and water. That is why you got a different reading. Ending at 1.000 isn't uncommon if you ferment to tolerance, but from what you've said, it sounds ...
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I typically return my sample after taking a reading. If your sanitation is appropriate then you wont have any issues. However, you mention that you rinse with water after sanitizing. I dont believe that's ideal, you are potentially reintroducing bacteria. Once soaked with the sanitising solution, you just leave it dry. That being said I use starsan rather ...
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You can also use a standard cooking baster to transfer liquid to your hydrometer vessel, but I'd recommend one that's made of glass and has a removable rubber bulb.
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