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The old permalinks still work because the rewrite rules that support those permalinks still exist. When you register a post type, setting the rewrite argument generates the rules to resolve incoming requests. Rather than adding new rules in addition to the originals, just alter the original post type registration.


You should be able to use category_name=$matches[1] instead of cat=$matches[1] Generally speaking, you can use any built-in public query variable and custom ones, after some additional work, see the add_rewrite_rule() codex entry for more information.


Let me say beforehand that when using add_rewrite_rule() nothing is written to the htaccess file. Rewrite rules are stored in the database and handled by WordPress internally on PHP level. TL;DR: Rewrite rules do persist after plugin deletion, but probably not the way you'd expect it. When using add_rewrite_rule these rules are added in the options table ...

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