When you buy a share of XYZ, there is a record of it in your name (or your broker's name) at the DTC. If that company changes its CUSIP (or gets bought out, or whatever), the legitimate records at the DTC get updated. If you had an illegitimate record, you won't get the replacement shares. Eventually you or your broker would realize this, and raise hell.
Incidentally, how many of you have ever had this problem? None. That's because these "fake shares" and "naked shorts" are conspiracy theories and legends and don't actually happen. It's also why the SEC seems to be "in on the conspiracy" to such folks. No, the reason the SEC doesn't do anything is because there is no conspiracy. They're tired of getting letters from retail whack-jobs complaining about naked shorting.
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