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The new permalink structure is only saved when
WP_Rewrite::flush_rules()
is called. Because this is an expensive operation (calculating the new rules and saving them to the database), you shouldt do it on every
init
call, but only when you change the structure. The custom post type however must be registered at every
init
call, since it is saved in a PHP array in memory,t in the database (which is why it forgot the custom post when you switched themes: the permalink structure still existed but referred to a custom post type that wast loaded, giving an error).
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