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You have to rerun the ceon_uri_mapping_installation_check.php. I get that. But after updating my .htaccess, I'm still getting 404s with every combination of the final rewrite rule.

RewriteRule...

If I put a store with this mod in a subdirectory, none of the URIs work anymore.

mysite.com/Category works fine but
mysite.com/upgrade/Category fails

Has anyone else dealt with this?

Please update this mod with the new copy of includes/functions/html_output.php
from the November 2015 patches
https://www.zen-cart.com/showthread.php?218914-Security-Patches-for-v1-5-4-November-2015