You will still need to apply the updates.
I'm not sure if reinstalling CF in FLMM using a fresh download will also eliminate the need of the new updates. It doesn't help that the updates are daily due to how CF's Dynamic Universe works.
If you have to deactivate CF because you want to play another mod then return to CF one day without the need to update it again, then you can make a copy of the vanilla backup folder and use "Change FL Directory" in FLMM so it will work with that new copy of FL. That way you will have both CF and whatever mod you want.
Just keep in mind to change save game folder as well.
Ok, thanks for the heads up, Not talking about the the daily dynamic universe updates tho, Only the first initial updates .. it really takes my net balance a blow if I were to do it every time I activate deactivate it, is there any offline patches installer for this ?