I've seen metal sleeves or plates that are designed to make up for weakened or notched out wooden members by sistering them but of course I don't have the links anymore.
The engineering's already been done with these. Just elevate the rafter end with a lally column and bolt on the kit.
You may first want to survey how extensive your damage is.
I imagine that these spongy rafters have lost some height due to some crushing because of the load that they are under. If you measure all the heights, 20 or 30, you may see others that are significantly below average.
This is assuming all the new rafter dimensions were within a 1/16" or so, or maybe even less. The dimensions of batches of lumber are probably pretty consistent, except for length.