I’m a bit puzzled by your description, I have a VM-E and may be able to help, by shaft for the Z axis do you mean the horizontal shaft that has the handle on it, or the threaded screw that goes vertically into the base? A picture or two may help, I have a very small copy of the manual/parts list which may shed some light on the problem.
One thing is for certain don’t go hammering anything yet!
Edit After giving a little thought and re-reading your post I think you must be referring to the shaft which takes the raising handle, and in this case I would imagine that possibly the nut which holds the worm gear has come undone allowing the shaft to come out.It will only come out a short way as the key which engages with the worm will stop it coming out completely. I have taken a picture which comes from the very sparse and small manual currently sold by Myford for this machine. Of course i may have the wrong end of the stick but it might help. It is not a difficult job to remove the saddle to gain access to the nut to check, you may be able to see it looking up from underneath the knee just to check. If needed i can copy other bits of the manual. The nut is part no 80.