Hmm, wouldn't you have to pick up a pretty run-down fort with unhappy dwarfs every spring? I can't imagine them coming out of a year of fending for themselves in too great shape - likely gone sober for half a year, with no new clothes and only one or two types of food.
The biggest potential problem is the seed limit - it works embark-wide: if e.g. the 'other' fort has 200 pig tail seeds and no standing orders to plant them, your half of the fort will have zero seeds and no way to get any new ones apart from the autumn caravan - when it's too late to plant them.
The manager's job orders are split among all appropriate workshops on the entire embark; it may happen that the non-active fort ends up producing some items, or blocking a bunch of jobs for a long time, because the orders get sent to their workshops repeatedly. Landed nobles cannot be replaced, so if the other half of the fort has the baron's residence, you cannot talk with diplomats (and the other half will have to deal with the two leftover diplomats from last year). Finally, trade depots are notoriously tricky - if you have two active ones on the same embark, they can completely screw up caravans. I think that some automatically-assigned jobs like butchery as well as hauling occasionally get assigned to workshops or dwarfs who have no path to the job items, but i'm not too sure. If that was really what happened, it only slowed down the execution of jobs and didn't block them totally.
Depot and workshop problems can be avoided if overseers are required to 'f'orbid workshops and buildings that could cause problems (and you could do it yourself if the last overseer forgot).
Edit: i don't mean to discourage you, just trying to point out some problems that might need adressing in the rules before you start.