Bowditch was forced off at half-time with a groin injury in the league win at Notts County on New Year's Day and the forward is expected to miss out.
Izale McLeod, who re-signed for the club on Thursday, will not be available for the third-round tie at Hillsborough.
The Dons are awaiting ratification from the Football Association as to when the striker - the club's all-time leading goalscorer - can make his second debut.
McLeod, released by Portsmouth on Monday, collected a one-match suspension in his final appearance for Pompey.
The Dons have asked for written clarification on whether he will serve the ban this weekend, which manager Karl Robinson would probably prefer as McLeod is cup-tied and therefore ineligible against the Owls anyway.
Angelo Balanta (QPR), Ibra Sekajja (Crystal Palace) and Zeli Ismail (Wolves) have all completed their loan spells at stadium:mk and returned to their parent clubs.
George Baldock (hamstring), Tom Flanagan (broken foot) and Jabo Ibehre (abdominal) have returned from loan spells elsewhere but are all injured.
Right-back Jon Otsemobor is still nursing a groin injury, while midfielders Stephen Gleeson (broken foot) and Luke Chadwick (knee) remain long term casualties.
One shred of good news for Robinson is that on-loan Brighton midfielder Ryan Harley, impressive when making his debut against Notts County three days ago, is allowed to play in the FA Cup.