When using divide (CTRL + /), you are not really meant to draw both the bonus and each territory's full outline. If you are dividing bonuses into territories, you would not be drawing the actual territory but instead the line for each territory divide. Could you send an image of the object being divided and the object you're dividing with? Below is an example showing a simple random bonus and each dividing line. You can ignore the shades of grey; they are purely to show each resulting territory.
Notice the order the division happens. This is because the dividing line must pass completely
through the object (or beyond). I could not have done any division but the red one first, then
the blue, then green, then yellow.
The object you divide with should be a line 'on top of' the object being divided, and this 'object on top' (line) is what should be deleted after the division, leaving you with the bottom divided object.
The following image may help; it shows a few results of division when the dividing object is/isn't on top. Since your bonus is being completely deleted, I suspect yours could be case number 1. Again it would be more helpful if I could see what the problem is.
Notice how cases 2,4 and 6 are the desired effect, and the line is on top in each instance of 'before'.