As Dave stated, lining up the holes isn’t easy on the water but there is no problem removing the CB while afloat. However, most floor boards will prevent you from reaching the bolt. Though water ingress is minimal (it takes hours to flood the boat) removing the back benches, the floor boards, and you know what is unnecessary difficult while afloat.
It is a fairly easy job ashore provided the mast is still up. Find yourself a soft lawn or some soft sand (beach). Then start with removing the back benches, the floor boards and any loose parts. Next slide the boat of its trolley into the grass. Then put it on its side by pulling the shrouds and weighing the mast down with something heavy to prevent the boat from accidentally rising again. (A case of beer will do fine, specially if friends are helping 😉
After you removed or inserted the CB the boat is righted slowly again by pulling the shrouds all the way until she is upright again. Then the boat is slid back on the trolley. Though it can be put on the trolley again by one person and a rope purchase, you may want he help of a friend or two for this. Have your friends lift the bow as high as possible while you push the trolley under the boat as far as it will go. Then one person holds the front of the trolley in place while two others push the boat at the transom forward.
This way the whole process of removing the CB takes less then five minutes and is much safer that fooling around with stacks of tires, work mates, chairs or other improvised scaffoldings. If you cant find a suitable lawn use fenders and/or blankets.