Avamar upgrade and missed emails

Hello. We are in the process of migrating our Exchange to 2013. In that same process, we built a new SourceOne server version 7.1.2.2075.  Our previous version was 6.7.0.3175.  The old server is still there. All mailboxes were supposed to have had their emails pulled back into their mailbox, mailbox migrated and then pulled in the new sourceone.  The last part is still in progress.  It appears that maybe a few users will missed before they were moved over to Exchange 2013 because they are still seeing shortcuts for all mail over 90 days and it points to the old server.  Most users have their email back in their mailbox.  I see the emails in the old sourceone server but I cannot search by user since that one was linked to the old mail server.  I can only search by date.  I cannot restore to a mailbox because I cannot see anyone on the new Exchange 2013.  Is there anyway to get their email back to them? The two sourceone systems are in the process of replicating but one user that has already replicated shows some of his old email but not the ones that are still showing a shortcut to the old system.  So I am not sure it will pull over the index to them or pull them over at all.  I am really in a bind here and any suggestions would be greatly appreciated.