Let's say we have a swarm1 (1 manager and 2 workers), I am going to back up this swarm on a daily basis, so if there is a problem some day, I could restore all the swarm to a new one (swarm2 = 1 manager and 2 workers too).
I followed what described here but it seems that while restoring, the new manager get the same token as the old manager, as a result : the 2 workers get disconnected and I end up with a new swarm2 with 1 manager and 0 worker.
Any ideas / solution?
I don't recommend restoring workers. Assuming you've only lost your single manager, just docker swarm leave on the workers, then join again. Then on the manager you can always cleanup old workers later (does not affect uptime) with docker node rm.
Note that if you loose the manager quorum, this doesn't mean the apps you're running go down, so you'll want to keep your workers up and providing your apps to your users until you fix your manager.
If your last manager fails or you lose quorum, then focus on restoring the raft DB so the swarm manager has quorum again. Then rejoin workers, or create new workers in parallel and only shutdown old workers when new ones are running your app. Here's a great talk by Laura Frank that goes into it at DockerCon.