Corrupted Index
The emails are not deleted from disk, the index is corrupted.
Resolution: Reindex all your volumes
In Journal Account
Архива ran out of diskspace. As such it marked the missing emails as unread. They may be sitting in the journal account
Resolution: Use a mail client such as Outlook / Mozilla Thunderbird to login to the Journal mailbox via IMAP. Mark any emails in there as unread.
Bad Encryption Parameters
The emails are present but they are encrypted using a different encryption key
Resolution: In this case, you need to use the reencrypt utility to normalize all volumes to use the same encryption key.
Bad Retention Rule
There is retention rule enabled that caused the emails to be deleted.
Resolution: Perform an Audit Search to see if the emails in question were deleted by the retention rule
Explicit Deletion
The emails were explicitly deleted by a user in the search interface
Resolution: Perform an Audit Search to see if the emails in question were deleted by a user
File System Delete
The emails were physically deleted from the file system (outside of Архива)
Resolution:Not much we can do here.