Honestly, I would probably leave it in. Assuming it's cotton batting, it will crinkle once it's washed/dried a few times & won't be terribly noticeable. The lesson I've learned to prevent that problem is always, always, always to SITD the entire quilt before I start doing any of my FMQ. That way, any extra fullness will be pushed to the edges rather than getting trapped between stitching lines.