I assume that you are referring to the right hand bearing cone. It sometimes gets dislodged from its normal position against the flange shoulder because in removing the spindle, the outer right hand dust cover is brought out early in the removal procedure by the right hand spindle bearing cone. Most of the time, it takes more force to move the cone than it does to press out the cover. I would have to say that if anyone removed the spindle without removing or at least moving the cover, either the spindle OD at the flange is undersized or the cone ID is oversized or possibly both.
What you will need to do before reassembly is to get a piece of pipe or structural tubing that is a sliding fit over the spindle and up against the cone and press the cone back up against the shoulder. Note that it is much better while pressing the cone back into position to support the spindle by the surface of the shoulder rather than to set the spindle on its threaded nose.