COBRAS calls the SQLSyncSvr on the Unity back end which does all the directory hooking here - you can look in the SQLSyncSvrxxx log file found in the \commserver\logs file to see it searching first for the DirectoryID then by UID/Alias to find the user in the directory.
Not quite sure how you have multiple mailboxes for a single user right off hand - but the linkage here is all up stream from the COBRAS restore itself.
These are the paths to get to each CCX logs through CLI. They may be helpful if you are having issues accessing RTMT or downloading logs through it.
If you want to download them you have to prefix "file get " and you can add one of the options (re...