Any target you can physically upgrade that still has an agent installed is not a concern here. Its the clients that no longer exist that should be deconfigured completely as you have no way of physically upgrading them. If you have an agent installed , just perform a normal upgrade of it and you will be good here with that one !
Here is the documentation on the 'upgrade of deconfigured clients':
During a CommServe upgrade, are deconfigured clients also upgraded?
If the CommServe software is upgraded to a new software release, any deconfigured clients from up to two prior releases will be automatically upgraded to the same software release. Thus, if a deconfigured client must be reinstalled, it will need to be reinstalled using the installation package for the same software release as the CommServe.
So the client (with the mailbox agent) you are restoring from also has the Mailbox Archiver agent installed or is that just the destination? May need a support case here to evaluate all options. As noted, the mailbox archiver agent cannot be upgraded, but that client also will not be upgraded if it cant be (which means all agents on it are required to be upgraded so an unsupported agent will block it from the upgrade here).
If the mailbox archiver agent is seperate from the mailbox agent that you are browsing from, than you should be ok here. Here is how I understand it (and please correct me where I am wrong):
mifv-exch3 - Exchange Mailbox agent only (you can upgrade this to v11 and restore using the separate PST option for this one)
mifv-exch2 - Exchange Mailbox Archiver agent (you cannot upgrade this client to v11 and are stuck with restoring to a single PST per job)
mel-ndc-exch01 - Exchange Mailbox and Exchange mailbox archiver agent (you cannot upgrade this client to v11 since it has the mailbox archiver agent BUT is the mailbox archiver agent only here to facilitate restores? if so we can get around this by deleting the mailbox archiver agent --- we could than stand up the mailbox archiver agent on a separate instance or server to be able to restore to it)