If removing the old calk, be very, very careful to not cut the membrane. I replaced the exhaust fan / vent on the ceiling / roof above the kitchen a few months ago. I was careful to remove the old one, but in order to remove it I had to work to remove the old calking. What I did not realize until I was able to lift the old fan housing free from the roof, I also cut the rubber roof. Mine is an Alpha. The new fan fit identical to the old one, except now, there was no rubber roof under the new fan itself.
My solution was to spread a very wide layer of new "Alpha" calking over the edge of the rubber and onto the wood roof that was no exposed. I then placed the new fan on top of it, screwed it down. Then went over with a second layer of Alpha calking over both the first layer of calk on the rubber and overlapped it on the base of the fan.
What I ended up with was about 3/4 of an inch thick of calking around the new roof fan. It must have worked, because the rubber around the new fan has held, never pulled up after a few thousand miles of travel on the road since.
So, if you remove the old, that membrane is VERY easy to tear and it's VERY easy to cut without even knowing it.
I have always advised to never remove the old for this very reason. Unfortunately, I had to pull it away to unearth the base of the fan assembly on the roof. Removing the edging and then attempting to clean off the old calk (just) could bigger problems than simply putting new directly over the top of the old, after cleaning the old real good (which is the way I've always taken care of mine).
