I suspect that your best option is to export va_countries and va_tax, update these and import them back into your database?
That should not take so long to do.
We also have to apply VAT to all exports but we only supply across Europe so doing it in 'admin' was no so difficult but I realize that this would be a crazy route for the whole world.
There was also the matter of VAT rate change recently - I had to update each country, of course.
Chris
http://www.malikstores.co.uk/