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Karl Robinson’s first game in charge of Charlton ended in a goalless stalemate on Saturday.
The Addicks boss, who took over on Monday was up against his former club in the second round of the FA Cup.
But the two sides will have to do it all again after a 0-0 draw, although it means that the Addicks will feature in Monday night’s third round draw.
Charlton’s best opening of a quiet first half came just before the interval when Nicky Ajose just failed to pick out Jordan Botaka.
MK Dons enjoyed plenty of possession but had rarely forced keeper Dillon Phillips into action – his best save coming to deny George Baldock.
After the break Josh Magennis went through but keeper David Martin saved well and Ajose was unable to convert the rebound.
Charlton gained in confidence and Magennis went close again.
MK Dons had a goal disallowed with 20 minutes left when Bowditch had an effort ruled out for offside.
The visitors nearly won the tie at the death but after Bowditch missed his kick, Ryan Colclough was unable to convert and then Bowditch’s effort was cleared off the line by former Gills midfielder Andrew Crofts.