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It seems like you need to review and optimize your backup concept. So you have a "mail/" directory on server1 and server2, both are in a cluster. The directory is configured to be symmetrical.
Some remarks that would help in your situation:
Users with homeserver1 should have mail files in a directory called "mail1", users on server2 will use "mail2". You can then back up the data on the primary server only because you know that all files in directory "mail1" belong to a specific server.
Make sure to DAOS and rethink your backup concept. For DAOS you only need incremental backups throughout the month and maybe one fullbackup a month or quarter
Depending on what backup software you are using, use an agent in Domino to loop all person documents of the "current" server and create a local *.txt file that is listing all file names of users where the home server is the current server. This file will be used to feed your backup program with the information what to back up.
I hope you're talking abotu Active-Active cluster members.