Flynn sustained a hamstring injury during Monday's home win over Aldershot and could miss the final game of the season next week against Crewe.
Gareth Evans replaced Flynn out wide on the right and is expected to retain his place in the side, with Jon Worthington and David Syers back in central midfield and Omar Daley on the left.
Midfielder Tom Adeyemi has a chance of featuring at some stage. The teenager has been receiving treatment for a thigh injury back at parent club Norwich, but is hoping to return after missing the last three matches.
Winger Kevin Ellison is still struggling with his thigh injury, which has kept him sidelined since mid-March, but he too is hoping to be included in the squad.
Peter Jackson's side require another point from their final two games to guarantee League Two football next season.
Source: PA
Source: PA