The logs show something like this for us:
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03/07/17 16:59:31 Failed to truncate index: \\directorybusiness.live\iis\MailEnable Config\Postoffices\domain.com\MAILROOT\user\INBOX. A file error occurred when opening file (32).
03/07/17 16:59:31 [Thread:12800]StreamXMLStoreIndexSerialiser::SerialiseHook Elapse: 265, Item= \\directorybusiness.live\iis\MailEnable Config\Postoffices\domain.com\MAILROOT\user\INBOX, Count=810
03/07/17 16:59:31 [Thread:12800]StreamXMLStoreIndexSerialiser::DeserialiseHook Elapse: 62, Item= \\directorybusiness.live\iis\MailEnable Config\Postoffices\domain.com\MAILROOT\user\INBOX\_index.xml, Count=810
03/07/17 16:59:31 Failed to deserialise index: \\directorybusiness.live\iis\MailEnable Config\Postoffices\domain.com\MAILROOT\user\INBOX. Failed to restore backup index. RestoreSerialisationBackup returned:5
03/07/17 16:59:31 StoreIndex_Open::Error opening store index in: \\directorybusiness.live\iis\MailEnable Config\Postoffices\domain.com\MAILROOT\user\INBOX
03/07/17 16:59:31 ME-EXXXX: Warning: Failed to access activity file (\\directorybusiness.live\iis\MailEnable Config\Postoffices\domain.com\MAILROOT\user\_activity.tab) for input. Client connection already removed (2).
03/07/17 16:59:31  End of conversation. Removing connection. Session=706285040
03/07/17 16:59:31 CleanupNotificationThread:: Notification thread terminated.
Updating to 9.6.2 does seem to have lessened the frequency of this happening, but it has still happened on a couple of inboxes over the past week.
The "bad" copy of the index is actually complete, so we've been able to recover these inboxes manually each time. What appears to be the issue is that MailEnable is updating the index with the new data just fine, though in all these cases the new data is shorter than the old data, and MailEnable is then not truncating the file. This means that at the end of the file, there's a snippet of left-over data from the previous write, so the end of the file looks something like this:
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<SUBJECT>******* </SUBJECT><TO>"email@example.com" <firstname.lastname@example.org></TO></ELEMENT></BASEELEMENT>
E><READ>0</READ><RECEIVED>2017-03-09T16:54:06</RECEIVED><SIZE>4650</SIZE><STATE>0</STATE><SUBJECT>******* </SUBJECT><TO>"email@example.com" <firstname.lastname@example.org></TO></ELEMENT></BASEELEMENT>
Like I said, this has only started happening since we upgraded from 9.18 to 9.6.1, and has continued with a further upgrade to 9.6.2.
Could you please advise on how to prevent this issue from happening in the future?