Yes, it does make sense, and if I've understood the request correctly, yes, it's absolutely possible.
At a given time, you can only archive messages into one store for a given user - so whatever rule applies to that user can only have a single destination store.
But if you've previously archived messages into a different store, they are still accessible without any problems. So if, last year, you'd had a rule which archived messages to "Store 2009", then at the start of this year, you changed the rule to "Store 2010", all the messages in both stores are still accessible and searchable.
Compressing the timescales, something we've seen in a lot of deployments is people running a rule to match messages over (say) 5 years old first, going to one store, then changing the rule to 3 years and another store, and so on, then getting into a more normal routine once they've "caught up" with the backlog of old messages.
I hope that helps - let me know if I've misunderstood!