If protons decay, they don't come back -- the whole reason why the Standard Model lacks proton decay is in how it treats conservation of quark number, since there is no path for a proton's components to a lower-energy state. If that part of the Standard Model is not exactly correct, protons may decay, and the final products will generally be useless for structure-building (e.g. a Georgi-Glashow model proton decays into a pair of gammas and a positron, and it is not energetically favourable for an "anti-decay" back into a proton to occur).

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.