Don't try to remove all of the old medium - Some may just fall out, or you can rinse under the faucet or blast with a hose, pick out what comes easily. That approach will also pretty much wash out broken down/rotted medium. Then when pot it up in fresh medium (which will have lots of air) you will create a healthy environment for the roots that will pretty much stop any residual rot. I find that if I get 80-90% of the old stuff out, the rest totally doesn't matter. You can remove obviously rotten roots, but when in doubt leave them. It's often difficult to tell the good ones from the bad ones. It is much better to leave a less-than good root than to accidentally remove a new one - once you cut, you can't re-attach if you made a mistake.