Update product variations using MySQL.

update_product_variations.sql

UPDATE wp_postmeta as pm, wp_posts as p 
SET pm.meta_value = 500 /* <new price> */
WHERE pm.post_id = p.ID
AND p.post_type = 'product_variation' 
AND pm.meta_key = '_price' 
AND pm.meta_value = 1000 /* <old price> */
AND p.post_status = 'publish';