import bpy
from pdb import set_trace

# quick handy little lambdas
first = lambda l : l[0]
last = lambda l : l[-1]

def chunks(lst, n):
    for i in range(0, len(lst), n):
        yield lst[i:i+n]

def swap_ys(p1, p2):
    p1.co.y, p2.co.y = p2.co.y, p1.co.y

ob = bpy.context.object
fcurves = ob.animation_data.action.fcurves
fcrv = last([c for c in fcurves if c.select])
kps = fcrv.keyframe_points
kps = [kp for kp in kps if kp.select_control_point]
kps_pairs = list(chunks(kps, 2))


kps_pairs = filter(lambda l: len(l)>1, kps_pairs)

def swap_pair(pair):

    def get_handle_diff(pt):
        left_diff = pt.handle_left.y - pt.co.y
        right_diff = pt.handle_right.y - pt.co.y
        return left_diff, right_diff

    # get the handle relative diff in advance before swapping
    left_diff_0, right_diff_0 = get_handle_diff(pair[0])
    left_diff_1, right_diff_1 = get_handle_diff(pair[1])

    # do the coordinate swap
    y1, y2 = pair[0].co.y, pair[1].co.y
    pair[0].co.y, pair[1].co.y = y2, y1

    # update the handles
    pair[0].handle_left.y = pair[0].co.y + left_diff_0
    pair[0].handle_right.y = pair[0].co.y + right_diff_0


    pair[1].handle_left.y = pair[1].co.y + left_diff_1
    pair[1].handle_right.y = pair[1].co.y + right_diff_1



for pair in kps_pairs:
    swap_pair(pair)