Hi there,
Welcome to the QuickBooks Community. The program is designed to help you streamline your accounting using the powerful features offered in the program. I'll be happy to share more info and help steer you in the right direction.
In order to make sure we're both on the same page, could you elaborate more about how you're "changing everything"? Otherwise, when changing a tax code in QuickBooks say on a invoice, the changes will be applied on that specific invoice. Changes on tax codes only affects transactions going forward after the change. You'd have to manually change the tax codes on the older transactions if you'd like to change the taxes on them.
Let me know if this info helps. I'll be a message away in case you need help with anything else.
