There's no official announcement on the Football League website as yet, but it would seem unlikely that they would want to share the prize funds with the Conference clubs involved.
The news wouldn't have effected the Shots next season as they failed to make the top twelve after the disappointing season.
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Football League Trophy
The new deal is the biggest investment in the Trophy's twenty-three year history and looks set to end the deal with the Conference which found the clubs who finished in the top twelve invited to battle it out with their League One and League Two counterparts.