You could use the no_custom unit attribute to clear the custom battle rosters up while leaving the campaign unaffected.
EDIT: I'm an idiot. This wouldn't work if the same units are used by more than one faction in different capacities (i.e. one has it as a homeland MIC recruitment option that should be in custom battle, and another has the same unit as a regional MIC unit, that shouldn't be in custom battle)
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