As you point out, in an accelerating Universe, large scale structures will become more and more isolated. So at a certain point you will have gravitationally bound superclusters separated by very large voids and less and less filamentary structures.
Once isolated, we can then study the dynamics of these independent superclusters. On very large time scales, galaxies will collide and merge. After collisions you will tend to form elliptical galaxies. So I think that you will end up with a big single elliptical galaxy.
Then we can be interested in the future of the stars of these galaxies. First we currently see that the star formation rate has already peaked some billion years ago. So as the number of galaxies collision that usually targets star formation, the star formation rate will slowly continue to decrease. Moreover, as heavy elements (all elements apart from hydrogen and helium) are formed in stars, the future generation of stars will have more and more heavy elements. From the nuclear point of view, the most stable element is iron, so on very very large time scales light elements will be converted into iron, whereas heavy elements will decay into iron.
This is a little speculative, but I think that on large time scales, more and more interstellar gas and stars will fall at the center of the gravitational potential of super elliptical galaxy. So as the density will increase at the center, you will mechanically form a heavier and heavier supermassive black hole. Another interesting point is that we do not currently know whether proton are stable or not. So on time scales larger than $10^{30}$ years (see more details here) protons may naturally decay into lighter subatomic particles.
So maybe as $trightarrowinfty$ we will end up with supermassive black holes and light particles. But as you mentioned, black holes will themselves slowly lose mass by Hawking radiation. In the same time, the expansion rate may have increased significantly leading ultimately to isolated particles in an expanding Universe.
Note: this is an hypothetical scenario and there are a lot of unknowns
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