well that too...
like haggen and merlight said you don't have to change the version of the saved variables when you update your addon.
but i was under the impression you knew this already and had different needs. Maybe a bit more details on what you're up to ?

btw if you need to generate different files for your versions you may want to look at how Master Merchant does
I suppose he creates fake addons with just a save vars then he probably make their content global to use them in the main addon. Never used MM can't tell for sure. But if it is to extract data for your site, can be something to check too.