Hello Michael, I'm sorry to hear you're having so much trouble with the indexing right now! One thing that can cause indexes (and other files) to get out of sync like this would be sudden restarts of the server such as power failures or crashes, so I would be on the lookout for any signs of trouble server-wise  or anything that might hint at stability issues in general. One other possibility is that something IN those indexed messages might be causing trouble as well. Did you have any spam reported recently that adhere to a pattern? Because spam campaigns typically target entire machines/networks, I'm wondering if a message might have come through with some content in it that caused trouble for our indexing. 

As to the resolution of these problems; to rebuild all indexes at once is something that has been requested, but is not currently available in SmarterMail. You can purge the contents of each users' index/indexv2 folders (with SM services stopped) though, and then issue the reindex command from a domain administrator account for all users at once. This would require you impersonate each domain, but at the very least you can reindex all users at once form the Domain Settings>Accounts page. 

I do recommend doing this for one or two domains at a time though, as indexing can be resource-intensive depending on account contents. 

Kyle,

Thanks for the reply. I'll do it domain by domain on Sunday, based on who has contacted me. No, no spam reports, and no power outage that I know of.

Another question: once a reindexing task is started, is there anywhere to go to see this progress? I know that if we initiate a Mailbox Migration you can come back to the page to see how many messages have been brought over at that point, (though not an indication of how many total emails are present on the other server, which would be nice). Perhaps a page somewhere at the top admin level that shows a progress report of some kind? That would help admins know when it's ok to start another reindex, or report to the domain owner that their reindexing has completed.

Also, having "Reindex" as an option at the domain list level, logged in as the server admin would be handy, which would reindex ALL accounts, including each domain's primary admin. You'll note that the admin account can't be reindexed in your screen shot.

Thanks