You can try using "Booleans>Union" instead. I just tried this with a rough representation of what you did and it worked. Remember you can only choose TWO polygons at a time for this, so go slow! :-)

If all else fails, use "Difference" (as matt stated above), then create new cylinders to the same size as your original gun barrels and insert them in the holes created. Hope this helps!

Carry on...