Alton has been suffering with groin problems, but came through an hour of a practice match at Fulham last week and was looking forward to his reserve return.
He impressed during the first half against Chelsea, but felt slight pain and did not return for the second period as a precaution.
"We've got a concern over Alton," reported coach Colin Calderwood. "He wanted to go back out in the second half and see how he felt but, with the length of time he's been out and Chic (physio, Wilkinson) has been monitoring him during that time, there was no reason to take a chance.
"If it turns out he plays 45 minutes and is able to train with no problem then that will be a big benefit to him.
"That is the one downside we've got coming out of the game and he hope he hasn't done anything that will set him back too far."
The good news is that Ledley, Anthony and Darren played well and came through unscathed.
"For the amount of time Ledley has been out and the little amount of football he played, he slotted in and looked extremely comfortable," added Colin.
"Anthony played in a couple of positions for us and, when he has to, uses three or four different gears to everyone else. Anthony, Ledley and Darren all got 90 minutes in and we hope they feel okay over the next couple of days."
The returning Darren Anderton, Ledley King and Anthony Gardner all came through 90 minutes against Chelsea at Stevenage, but Alton Thelwell was withdrawn at half-time.