Can you replace an active Crimson Rite on a weapon? For example, if I have the Rite of the Flame activated on my longsword, can I use the Crimson Rite feature again and replace it with Rite of the Flame? Based on how I read the Blood Hunter subclass, the rite will last until "you finish a short or long rest, or if you aren’t holding the weapon at the end of your turn." 

So that means you can't deactivate the rite, right? You can deactivate it of course by sheathing your weapon but I mean you can't replace an active Crimson Rite with another one that you know., right?

I understand this is homebrew material, but I'm curious on your guys' thoughts and opinions. Of course, it does mean taking extra hemocraft damage if they can just deactivate and replace active rites but also it can mean versatility in a fight? Like if a Blood Hunter realizes that they have a rite which does damage that a creature they're fighting is vulnerable to, it would be a good idea to swap rites mid-fight. 

Having a Crimson Rite already on a weapon doesn't seem to stop you being able to put another one on it - but it does say a weapon can only have 1 active at a time. So I would say you can replace one rite with another just by using the feature again with a Bonus Action. You would have to roll another Hemocraft Die and take damage from it again - but I would absolutely say you don't have to disable the old rite first to do it.

If you are not in combat, just place the weapon on the ground for a moment and the crimson rite will fade. I guess you could do this even if you were in combat.

If you wanted to swap one with another, I agree with Emmber that a new rite would likely end/replace the old one.