if I understand you correctly, you have two email servers A and B. domainA is on A, and domainB is on B. You'd like to backup (from a filesystem perspective) files from A to B, and in the event of a failure, bring up domainA on B.
I don't think you can do this from the filesystem level (just like the opposite wouldn't work).
One possibility, however, is to create a "fake" domain called standbyDomainA on B, then use something like imapsync to synchronize all accounts from domainA to standbyDomainA regularly. This will then retain IMAP settings e.g. folders, tags etc.
On failure on server A, rename (using Zimbra GUI or CLI) standbyDomainA to domainA, and change your MX records to point to the B server, now hosting domainA as well as domainB.
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