Experience tells me that you won't have any issues re-using the main shaft. In an attempt to mitigate any influence the missing tooth might have on the retainer snap ring function, I would install said snap ring so that missing tooth is positioned 180* opposite the open end of the snap ring. As said above, I have used main shafts in racing applications with as many as 3 consecutive teeth missing without any incidents. My guess at cause is, heat treat tends to make the previously machined teeth exposed on the side of the retainer ring groove a bit brittle due to the surface area ratio of the exposed teeth to their mass. You should see what happens to those teeth when someone forgets to remove that snap ring prior to driving the main shaft, forward, out of the rear bearing. Additionally, I would recommend installing a "new" snap ring in that retainer groove simply to maximize it's clamping force on the base of the ring groove, thereby, limiting its ability to float around the groove.
