Refractometer calculators that predict ABV become wildly inaccurate when when the final gravity gets that low.
I experienced this when I was brewing a Brut IPA and the refractometer calculator (Sean Terrill's, which is quite good) kept telling me I had 4 or 5 points to go to 1.000. I measured with a hydrometer and turns out I was already at .998 or so.
However, it sounds like you for your purposes you could determine a Brix reading that would correspond with .990. IE if that number is 3 Brix, don't rely on the calculator and just wait until you hit 3 Brix; that would be reliable. But you'd have to test to see what that number is with your hydrometer for a given recipe. If your recipe changes (OG, fermentibilty, yeast, etc.), then that number would not be reliable anymore.
If you want to be safe, using the hydrometer is the best route.