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I'm not sure I understand the problem. Why do the permissions have to be changed in the first place? I assume you are going to be using the same usernames on the new server.
The permission for folders are copied, but the owner of the folders are not owner's name, instead of user id , there shows owner and groups are user id of old server.
So the main problem is if I create same username, the user id will not be same as old server.
I think I could just copy the passwd file the new server, but I'm afraid that could damage some softwares or resulting bad effect.
There should be no problems copying over the account/password files over to the new machine. You could even just cut the user accounts out of the old file, and append that to the file on the new server; so that the system accounts will not be changed, only the users.
Then just copy the mailboxes, and the permissions should still work.
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