He sat out the trip to Mansfield on Monday, and the club will get an expert opinion on the injury this week.
Iron boss Brian Laws said: "We will have him to a specialist this week to make sure there is no major damage in there.
"Whether it's a cartilage problem or a bursa behind the knee-cap we are not too sure at the moment.
"The knee is very, very sore after he landed on it heavily against Darlington."
Fellow defender Andy Crosby is also a doubt for the trip to Stamford Bridge with an Achilles injury.
He has been told to rest, meaning he could be forced to sit out the Cup game.
Loanee Neil Teggart suffered a rib injury during the warm-up to the game at Mansfield, and is also a doubt.