Look at pic 25.9 in Haynes.
The bolt is there to clamp the cases together around the gearbox shaft bearings and support and hold them in position.
So worst case scenario......Bearing becomes loose in operation and spins in its housing or if it is the locked end of the shaft it it becomes loose and it starts to float. Either way it could result in serious damage to the case set or gearbox internals. Alternatively there may still be enough compression between the case halves to hold the bearing and it may never come loose in the lifetime of the bike and never cause any problems. Its difficult to call either way but if there is no oil leaking from the hole or in the vicinity of the of joint and no additional noise or vibration its safe to assume the bearing is presently holding in position.
A good machine shop might be able to put a pilot hole down the axis of the remnant with a long series drill, then using a small screw-extracter thats been welded onto a length of stock bar to extend its length spin it out but again.........its an unknown.
The way I see it there are 3 options.
Cover up the damage and offload the bike.
Run with it as is, it might last it might not but if it does fail you will be looking at serious money to fix it, possibly a written off case set.
Bite the bullet, pull the engine out and deal with it now.
I would go with in this order but its your call