The struggling NRL club's great hope, Reed ruptured a tendon in his finger during Saturday's heavy loss to Newcastle and underwent surgery on Tuesday.
His absence meant Flanagan and Daniel Atkinson trained in the halves on Tuesday, the latter on return from a hand injury that had troubled him for the preceding weeks.
Interim coach Dean Young memorably handed 20-year-old Reed an NRL debut for his first game in charge on Anzac Day and had hoped to give him a run in the first-grade side.
Instead, Flanagan's exile has ended after two games as the Dragons hope to break a 13-game losing streak against ladder-leading Penrith during Magic Round on Sunday.
Flanagan had been listed on Young's bench since the Dragons parted ways with his father last month following a seven-game losing streak to begin the new year.
The younger Flanagan, contracted until the end of next year, has not made it onto the field in either of the side's losses under Young.
But Dragons co-captain Damien Cook has been impressed by Flanagan's attitude at a tumultuous time.
"His dad being coach, it'd be hard to go through, and the way he's carried himself around the club has been really good," said Cook, who plays his 250th NRL game against the Panthers.
"Not many people would ever have to go through that situation in the game, where the coach is their dad, plus you've spent a couple of weeks not starting.
"I feel for him. I've definitely been impressed with how he's handled it."
The Dragons expect to have an update on Reed's condition this week and are hopeful he may return sooner than the 12 weeks similar injuries can require post-surgery.
Some teammates and club staff were unaware of the severity of Reed's injury until training on Tuesday, with the young gun hiding his pain after the round-10 loss.
Cook expected Reed would remain level-headed amid the setback, which comes after 62-16 and 44-10 losses in his first two NRL games.
"Obviously it's been a tough start for him, great to get your debut in a massive game on Anzac Day and obviously it wasn't the way we wanted it to go," Cook said.
"He's at the start of his career, obviously he had that (halfback) spot and he was trying to really get a few games under his belt.
"I know the type of kid he is, I know how hard he works. He'll be back, better for it."
Dragons co-captain Clint Gutherson sat out of training on Tuesday but was named on Young's team sheet and will be monitored ahead of Magic Round.
Moses Suli's return from a back injury opens the fullback spot up for Gutherson, who had a tough afternoon moonlighting at right centre against the Knights.
Val Holmes remains at left centre after shaking off a shoulder complaint, but Mat Feagai's back issue brings Christian Tuipulotu onto a wing.
Back-up hooker Jacob Liddle, the club's best player in the Flanagan era, is still at least another week off returning from a hamstring issue.
