One possibility here would be to update the retroactive files through hook_cron() like Drupal does for search indexing. Have it query the DB for the data with say a 1,000 row limit each cron run. A simple select count(*) can tell you how many users or orders remain to be updated.

Then when you really need to apply the retroactive somewhere, you can just hit cron as many times as you need. Search indexing has a simple form that will call the same function from a form for easier use.