Well this seems to fix it. Not sure if this is the best way to do it so please enlighten me if I’m wrong:
By changing:
if ( $wp_rewrite->using_permalinks() ) $pagination['base'] = user_trailingslashit( trailingslashit( remove_query_arg( 's', get_pagenum_link( 1 ) ) ) . 'page/%#%/', 'paged' );
to:
if ( $wp_rewrite->using_permalinks() ) $_SERVER['REQUEST_URI'] = user_trailingslashit( trailingslashit( remove_query_arg( 's', get_pagenum_link( 1 ) ) ) . 'page/%#%/', 'paged' );
It’s working. Now all I have to do is to create a fall back if you enter a taxonomy from page 4 to the new taxonomy on page 1.
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