I agree with Jon - it would be best to migrate ALL data and then blast away the data that you don't need, rather than the other way around.
Although, if at all possible, get rid of as much data as possible first prior to migration. That's the best time to do it.
Note that you can selectively move data from one location to another, but this is something that we'd refer you to a CA Business Partner or CA Services to do, as it involves making sure that the data mapping/transformation is strictly done.
All in all, you're best to (a) clean up data first and (b) migrate.
Thanks, Kyle_R.