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Apparently, this works:

1. Copy each user folder from old_server_nbfiles/home into new_server_nbfiles/home. You have to decide which admin folder you keep, or maybe download all the old_server's admin worksheets and upload them into the new_server admin account. Similarly, solve the problem manually if there are different users in both servers with the same name. This might involve sending an email or who knows.
2. Load into a sage console the users.pickle file in the nbfiles.sagenb folder from both the old and the new server. This is a list with one entry per user. Merge both lists, but beware the admin account and the users in both servers with the same name. Your choices now should be compatible with the ones you made before. Use pickle.dump to save the new users.pickle that will go into the new_server nbfiles.sagenb folder.

The above was done while the servers were not running. It was one real server and a sample one. If I get more problems with the two real world servers, I'll post them here.