"We've had some really bad news with Francisco damaging his cruciate, this time on his left knee," reserves boss Gary Ablett told the club's official website.
"It was something really innocuous in training and as soon as he went down we saw the pain in his face and we feared the worst.
"He has had an operation and will be out for six months minimum unfortunately. Mentally, the boy is as strong a kid as you will ever meet in terms of what he's been through, and we are all doing our best to keep the lad going.
"Fran is probably as technically a gifted a player as we have in the reserve team squad and it's just unfortunate he's had these injuries."