The 21-year-old spent the first half of the campaign on loan at League Two leaders Gillingham.
His performances for the Gills earned him a call-up to the Northern Ireland Under-21 squad in November.
Flanagan, who has featured 28 times for the Dons' first team, will go straight into the Bees' squad for their trip to Accrington Stanley this weekend.
Restore Data
| Team | P | W | D | L | F | A | GD | PTS | |
| 1 | York City | 21 | 13 | 5 | 3 | 43 | 19 | 24 | 44 |
| 2 | Barnet | 21 | 14 | 2 | 5 | 42 | 24 | 18 | 44 |
| 3 | Forest Green RoversForest Green | 20 | 12 | 6 | 2 | 38 | 17 | 21 | 42 |
| 4 | Gateshead | 21 | 11 | 5 | 5 | 37 | 27 | 10 | 38 |
| 5 | Oldham AthleticOldham | 19 | 10 | 7 | 2 | 33 | 17 | 16 | 37 |
| 6 | Rochdale | 19 | 10 | 3 | 6 | 28 | 18 | 10 | 33 |
| 7 | Sutton UnitedSutton | 21 | 9 | 5 | 7 | 29 | 26 | 3 | 32 |
| 8 | AltrinchamAltrincham | 21 | 8 | 7 | 6 | 35 | 28 | 7 | 31 |
| 9 | Solihull MoorsSolihull | 21 | 9 | 4 | 8 | 37 | 34 | 3 | 31 |
| 10 | Yeovil TownYeovil | 21 | 9 | 4 | 8 | 24 | 22 | 2 | 31 |
| 11 | Halifax TownHalifax | 21 | 8 | 7 | 6 | 21 | 19 | 2 | 31 |
| 12 | Hartlepool UnitedHartlepool | 21 | 7 | 8 | 6 | 24 | 24 | 0 | 29 |
| 13 | Eastleigh | 20 | 7 | 7 | 6 | 27 | 26 | 1 | 28 |
| 14 | Southend UnitedSouthend | 21 | 6 | 8 | 7 | 24 | 24 | 0 | 26 |
| 15 | Dagenham & RedbridgeDag & Red | 20 | 6 | 7 | 7 | 34 | 26 | 8 | 25 |
| 16 | Tamworth | 19 | 7 | 4 | 8 | 22 | 33 | -11 | 25 |
| 17 | Aldershot TownAldershot | 21 | 5 | 7 | 9 | 28 | 35 | -7 | 22 |
| 18 | Woking | 21 | 5 | 6 | 10 | 19 | 28 | -9 | 21 |
| 19 | Fylde | 21 | 6 | 3 | 12 | 25 | 41 | -16 | 21 |
| 20 | WealdstoneWealdstone | 20 | 4 | 8 | 8 | 22 | 29 | -7 | 20 |
| 21 | Braintree TownBraintree | 21 | 5 | 5 | 11 | 18 | 28 | -10 | 20 |
| 22 | Maidenhead UnitedMaidenhead | 21 | 5 | 4 | 12 | 26 | 43 | -17 | 19 |
| 23 | Boston UnitedBoston | 21 | 3 | 6 | 12 | 19 | 36 | -17 | 15 |
| 24 | Ebbsfleet | 21 | 1 | 6 | 14 | 15 | 46 | -31 | 9 |
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