First off, the Sun will not become a supernova. It's not a big enough star.The Sun WILL become a red giant. When this happens, the internal pressure of the Sun will counteract its gravity to an extent, and so the density will decrease. It can't just destroy mass like that, which is why it expands to become a giant star. I think this may be what you are asking, how the atoms in the Sun will be able to lower the pressure: they will just take up more volume.
Now, the Sun will genuinely lose mass during all of this, because the outer layers of the Sun will come off into space. Eventually, however, the heat source will die, and the star will collapse to become a white dwarf, which is a lot smaller than the Sun is even today volume-wise.
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