Q: Mail seems to have lost mail message content since upgrading to el capitan

OK. I seem to have solved, or at least recovered from, the problem.

This is what I did:

1. I located the Personal Folders.mbox folder  in ~/Library/Mail/V3/Mailboxes.
2. I copied the whole thing to the desktop.
3. I then copied each of the lowest level *.mbox folders that it contained to my desktop. (Their hierarchy mirrored that of my Mail personal folders)
4. I also copied any *.mbox folders that were not the lowest level (this was necessary because they contained mail messages that were not  inside the lower level folders. )
5. Tip: to make it tractable i recreated using nested normal folders on my desktop a hierarchy  that matched what i had in Mail. (this is not essential but if like me you have a lot of mail folders in a hierachy it helps keep track of where they need to go and to make sure you have covered all of them
6. I then Imported each *.mbox folder in turn. (Using File... Import Mailboxes) It is possible to select several at once but i mostly did them one at a time. Mail creates a separate "Import" folder in mail for every import you do.
7. i then moved, using drag and drop,  the contents of each of these imported mail boxes into the appropriate place in my original Personal Folders hierarchy.
   • I did  this by selecting all of the messages in each imported mail box and raging these to the appropriate folder.
   • I noticed that even though i was moving some more recent messages that were already visible in my personal folders there did not appear to end up visibly duplicated.
8. I repeated the same process but for each of the "Sent" folders for each of my POP3 mail accounts. (which are stored in ~/Library/Mail/V3/POP-username@maildomain.com, where username@maildomain.com is replaced by the email address of your own particular email account)
9. I did;t do this but if you had lots of emails in your inbox or drafts or junk or deleted folders you could repeat for the *.mbox files that represent these. (I keep these empty so did not need to do this step)
10. I then deleted the now empty Import  folders.
11. Bingo! my mail was all back and visible.

Caveat: I suspect that what i should have done, in hindsight,  is created a completely new hierarchy of Personal folders rather than repopulate the old one. I worry that I might have some stored up issue that makes the mailbox more prone to future corruption but i have no evidence for that. But so far it is working fine.

Notes:

• I checked the size of the resultant active Personal Folder.mbox folder in ~/Library/Mail/V3/Mailboxes expecting it to have increased in size. BUT it was exactly the same size as it was before!
• That is good news because i was expecting that it would still contain the original emails but in some hidden state.
• The fact that it did't increase in size and the fact that the drag and dropping of all the mail messages from the Import folders (step 7) to my original mail folders didn't result in any duplicates makes me think that what is actually go here is that this process reconnects everything rather than actually duplicating importing more data.

How long this takes obviously depends on how complex the hierarchy is in your Personal Folders. I have 89 folders with nesting of up to 3 levels deep and it too me several hours of work.

I will repost if i find any problems with the result. But so far after 24 hours i have encountered no problems or side effects.

I still don't quite know what caused this under the hood other than the El Capitan Upgrade. It is possible that the way i went about adding back in my missing email accounts and the resultant re-download of all the messages that were still sitting on the POP3 servers might have caused this but i will never know.

This is is the first MacOX upgrade that i have ever had this problem with. After all of the public Beta testing that went on (and which I had stayed away from to avoid such issues!) I would have hoped the EL Capitan upgrade experience to be better than most. It is disappointing and at times heart stopping that it was so stressful!

I hope this helps others who may have experienced the same issue.

I had tried that but when I tried to rebuild the mailbox it just lost the few emails that were visible in it.

An update: I have just, foolishly upgraded to the latest update to El Capitan 10.11.1 and it has completely messed up all of my personal folders again.. they have once more disappeared!

If you have had this problem with the original EL Capitan update and fixed it using my method above I'd recommend NOT upgrading to 10.11.1.

I am really fed up with all these problems. El Capitan has been the worst upgrade experience I have ever had with MacOS X, and i have been through them all. Unbelievably bad!

Grrr!

macOS Sierra upgrade seems to have recreated the problem with Mail again! The 2nd and subsuquent dot releases of El Capitan seem to have contained a fix for this problem. But it appears that Sierra has not included what ever the Apple fix was.. or introduced some other bug that gives almost identical results.

Any one else found that they can no longer see the emails in their personal folders since the Sierra upgrade?