Larch isn't under active development anymore (I long ago stopped having a need for it myself), but even if it were, two-way sync is a big can of worms to open up. It's very hard to get right, and when you don't get it right, people can lose precious data. One of my fundamental principles in developing Larch was that I never ever wanted to lose anyone's data due to a bug, which is why Larch is designed never to delete anything on the destination server.
So, no, it's not in Larch's future, and I wouldn't accept a pull request that implements it. That said, Larch is open source, so feel free to fork it, change the name, and have your way with it! :)
For your specific case, I'd recommend doing a staggered migration. Divide your users into groups and schedule a time for each group when their accounts on the old server will become read-only and new mail will start being delivered to the new server. As soon as a user's account on the old server becomes read-only, start migrating it to the new server with Larch. Larch will happily migrate all the old messages to the new server even while new messages are being delivered there, and the only inconvenience to the user will be that they'll need to wait for the migration to finish before all their old messages will be available to them.
(you could also perform the migration all at once for all users, but that may or may not be feasible depending on how many users you're migrating)
- Ryan