There would possibly be a small amount of sugar loss, yes. However, the majority of the loss would be water. The reason for this is that imparting a vacuum will cause the molecules of the highest vapor pressure in the mixture to volatilize and be removed.

Think of it in the same way as distillation. You separate ethanol from water by heating it. Even though they're mixed, the ethanol has a much lower boiling point than water so it boils off while the water remains (like in a reduction). This can get tricky with ethanol and water because the mixture is azeotropic but that's a different issue.

Outside of adding heat, the other way to boil something is to remove pressure (to an extent). When you apply a vacuum to something, water actually boils off, even though it doesn't get hot, because you're decreasing pressure. The phenomenon is described by the ideal gas law and it's the same reason that water boils at a lower temperature in the mountains than it would in New Orleans.

Where this relates to this is that when a vacuum is applied under the conditions we're capable of, water will boil but the sugar will not. As the water is boiled off by the vacuum, the sugar remains behind and is concentrated. It's like if you boil salt water - notice that the water boils off and the salt is left behind and forms crystals. It's a similar thing with applying a vacuum to watermelon - the water will boil off (with some juice possibly being lost just from the force of the vacuum sucking in the liquid) but the sugar molecules wont. They'll remain and increase in concentration.