Once Nate Bremer (Solaris) had flooded fields and many peonies rotted. When I asked him about my situation with rotten roots he did not recommend to pot the roots because the fungus is always in the soil and peonies in pots get it easily. I saved what he replied: Bleach mixed with water (1 part bleach to 10 parts water): To disinfect the roots are dug, divided and all roots are removed leaving the crown. Crowns are power washed and then submerged in bleach solution for 45 minutes and then washed again and dried. After all this the crowns have no stems and look almost white. The bleach kills nearly every disease organism. After all of that they get planted in a clean field. All the roots get removed. Sounds odd but the plants quickly regrow new young roots that have no disease. Old storage roots often harbor disease and are of little to no help. Plants do not look good the first year, but by the second year are vigorous growers.
You might not need to remove all roots but cut them generously so nothing even close to start rotting is remained. Good luck!
