If you just want to update the counts of posts in each term, wp_update_term_count_now( $terms, $taxonomy ) should do it… just pass the terms affected as an array and run it once for each taxonomy you have.
You can also call wp_defer_term_counting( true ) before inserting new rows, and then after adding your posts, catch up on the counts by calling wp_defer_term_counting( false ).
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