I am talking about very long term applications, which (it seems?) you aren't trying to address.
For example: yes, to run a reversible computer without waste heat you need to actually uncompute intermediate results. This introduces time overhead which is generally unacceptable for real applications in the modern world, where negentropy is abundant. But what does this have to do with the long term capability of the universe for computation?
I think if you realistically want to run a reversible computer, you need to uncompute regardless, because otherwise your space is non-reusable, becoming only as useful as time.
This post may be interesting to some LWers.
In summary: it looks like our universe can support reversible computers which don't create entropy. Reversible computers can simulate irreversible computers, with pretty mild time and space blowup. So if moral value comes from computation, negentropy probably won't be such an important resource for distant future folks, and if the universe lasts a long time we may be able to simulate astronomically long-lived civilizations (easily 10^(10^25) clock cycles, using current estimates and neglecting other obstructions).
Has this been discussed before, and/or is there some reason that it doesn't work or isn't relevant? I suspect that this consideration won't matter in the long run, but it is at least interesting and seems to significantly deflate (long-run) concerns about entropy.