I think I found the problem. The upgrade program is looking for the file patch.pl in the xcart directory, and it wasn't there. So I found one from the 4.0.12-13 upgrade and placed it in the xcart directory.
Now I can run the 4.0.16-17 patch. I looked at the patch.pl file from 4.0.12-13 and it doesn't appear to be specific to that upgrade, just coding for running patches.
Should work (always a backup if not)
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x-cart Gold 4.7.4
RedHat Linux 7.2; Pearl 5.20.2; PHP 5.5.26; MySQL 5.6.27, server 5.1.54;
Ruby 2.1.5p273; Python 3.4.2;
Several mods in menu and skin, BSCE shipping-per-product, CDSEO Pro
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