I am wondering, if i start a new game but this time in Classic Mode rather than story mode does this remove my story mode save and if so is there a way to import my story mode data to classic mode?
You're only allowed one save per copy of the game. Starting a new game in classic mode will remove your story mode save and data. If you haven't beaten the game you won't be able to import data.
There is a way around this, though--use the 3DS's save backup feature to create a backup save for your Story Mode game, allowing you to play Classic Mode.