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I have two sites, A and B. In each site I have a mail server and DNS. On DNS I have two MX records : MX 5 MX 10

DNS zone are integrated in AD.

These two site are connected over VPN. I need to users from site A to send mail over mail01 and user from site B sent mail over mail02, and when one of mail servers down all user sent mail over second available mail server.

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That's not possible without having different "perspectives" of the zone from the different sites, which won't happen with your current configuration.

If you have flexibility to make large changes to the name resolution configuration, then you could have different zones in the different sites, or BIND servers with different views.. or potentially some other creative trickery outside DNS like having a NAT in each site's firewall that directs a special IP to the local mail server.

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