I lost custom fees when apply pricing rules I'm using commerce fees modules to add fees when I create orders manually from the backoffice, but click when I click apply pricing rules I lost the added fees. If I add fees (custom fees line item) after applying pricing rules, the VAT taxe be applyed to the unit price only.
Any help please.
Are you using Rules 7.x-2.8? There's a known issue with that release that breaks the application of pricing rules: https://www.drupal.org/node/2403851

The latest development build of Rules may fix the issue: https://www.drupal.org/node/2324587