Online Archiving Folder Structure Not Matching Source

We have a user that has online archiving activated. Recently when I tried to search for a email older than a year (which is our retention policy), I noticed that the Online Archiving folder was missing many of the subfolders in the user's main email folder. The only thing I could think of would was user intervention, but I asked the user and they did not delete or move any subfolders in the Online Archive folder. I even searched unsuccessfully to see of any folders were inadvertently moved to a different location. Is it possible there is a syncing error with the archive? If the Online Archive folder doesn't have a matching subfolder, wouldn't it create it whenever a message needs to be archived into a subfolder? I'm worried that we may be losing emails if the matching subfolder does not exist in the Online Archive folder. Any insight would be appreciated. Thanks!