The 28-year-old midfielder has been out of action since suffering a torn anterior cruciate ligament in the 2013 CONCACAF Gold Cup Final.
It is understood that Holden is still at least another week away from returning to full training.
The former Houston Dynamo star, whose current contract expires this summer, is also in line for a contract extension regardless of whether he makes it back into the first team before their season ends.
The new deal is still in the works, according to the club.
"I won't make a judgment on Stuart's playing to give him a new contract"
Freedman told The Bolton News last week.
"However, I have spoken to him. I will keep that conversation private on what I have said about next year, but what I said did ease him a little bit."