If YunoHost's archive system is convenient enough to migrate a server, you can also migrate from server to server with rsync.
If you merge 2 servers together, you will need to recreate the users, domains and permissions of the first server on the destination server. Then you can restore app by app.
There is a limitation concerning apps that have the same ID. It will not be possible to restore them easily. Also be careful not to delete the eponymous app from the destination server :/
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