Duff had a damaged lateral ligament and hamstring tendon repaired in the first round of surgery, but will also need a second op in a couple of months' time to correct cruciate ligament damage.
Clarets boss Steve Cotterill said: "Michael has just had an operation and his lateral ligament has snapped off the bone. That one has been sutured.
"His hamstring tendon has snapped off a bone on the lateral side, so that has also been sutured in.
"But the worst part of it is he has probably got to go back in about six to eight weeks, because he has snapped his cruciate ligament as well."