The luckless 28-year-old underwent surgery on Monday to deal with the latest problem in his knee and may not play again in 2014.
After four major setbacks - which have restricted him to just five Bolton appearances in three years - there will be those who query whether Holden will ever play again after his latest comeback attempt earlier this month lasted just 23 minutes.
Yet the United States international retains a strong desire to try and play professional football again, a passion which Freedman admires.
So while Holden's contract is up this summer, Freedman has assured the midfielder his time at Bolton is not necessarily up.
"Stuart, first and foremost, has his operation to deal with," said the Scot.
"Then when he deals with the operation we'll see where we go from that.
"It (his contract) is not something that's top of Stuart's list. He'll be back here for pre-season and hopefully we see him here running around and then we can make a decision.
"But if he wants to be, he's always welcome here. As long as I'm the manager he's always welcome here and he's always going to be here. With the injury, we just need to make sure he's right first."