Not sure what state you are in but I can't imagine any state putting a time limit on marital separation. That just seems weird to me. And as long as there aren't any countermanding court orders (ie, restraining orders), I also cannot imagine any state mandating that two 'separated' parties not reside in the same domicile, again, absent any supervening court requirements. Having been through a separation, I can't imagine why anyone would ever actually want to do that, though. But that's a whole other deal.
If this information is for you, I strongly recommend you find the best family law/divorce attorney you can afford and go over the situation with them. They are worth every penny.