Kick start removal

The teeth on my kick start rounded today so thought id better make sure the shaft inside the engine casing was fine. So drained oil and coolant and remoed all bolts for the side casing. But the shaft on the water pump came with it. So will the timing now be messed up or can i fit the shaft back in and put it back together or is there alot more than that? Any help would be appreiciated. Thanks