If you have access to a vacuum chamber, you could make it so the balloon won’t float and you can weigh it on a scale. You don’t need a full vacuum to achieve this. You could even fill the chamber with hydrogen, just needs to be less dense than the balloon.
Another way is to weigh an empty balloon, weigh a helium tank, then fill the balloon and add the difference in weight to the empty balloon weight and you have the weight of the filled balloon.
It’s not going to have negative weight and the buoyant forces pushing it upward are going to be greater than the weight so you cannot use that number directly.
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