> Either way it'd be an unqualified success.
Certainly. I'm just picking nits on the math.
That is, when the protons are gone, so is chemistry, electronics, and so forth.
Of course lots of protons -- likely the vast majority of them -- will end up in stellar collapse remnants anyway, and in the black hole cases you're also not getting the protons back, whether or not they would eventually have decayed. The rest will be in an extremely tenuous gas and dust far outside the black-hole-dominated remnants of no-longer-star-forming galaxies, and most of that will be neutral hydrogen (and in that case if the proton decays, the residual positive charge will annihilate the electron, so all you have left is light flashing off in several random directions).
"Mining" for new components in the extreme future looks like a losing proposition even without proton decay; with proton decay, you run out of usable material all the sooner.