Mails missing or invisible in personal folders since Sierra upgrade

My situation was a little different after recently upgrading from 10.11 (El Capitan) to macOS 10.12 (Sierra) so I thought it worth mentioning in case it saves time for someone else.

The first time I launched Mail after the upgrade, I got the dialog telling me mail would be migrated. That finished quickly, and the main Mail window opened, but it was only showing a few of my mailboxes, and none of my smart mailboxes, and only a few of my original folders. In total, it was showing only about 20% of my original mailboxes in the various subfolders.

I was going to try the restore in the V4 folder like dianeoforegon and muzz63, but I went searching in the V4 folder, I found a lot of mailboxes that were not showing in Mail before. So I launched Mail again, and this time all the folders were there, including smart mailboxes! I don't know if the migration was being done in the background (doubtful), but in my case, it was enough to quit and relaunch Mail (and a restart was in there, too, for other reasons).

In short, be patient and maybe your mailboxes will automagically reappear the next time you launch Mail.

January 2017,

I upgraded to Mac Sierra this month and lost all messages in my folders.

for a couple of days I fiddled about until i read Ibz which talked about Mail

filters and a glitch when installing Sierra.

I followed the instruction and bingo all is well

Go to Mail - View - disable filters, then go to each Mailbox , click on it and then Command L,

worked perfectly.

Thank you very very much

I have mail missing from "on my mac" folders...the folder is there but empty...and the account no longer exists so I can't access it any more...help...

looking at the above...I can't find

~/Library/Mail/V3 folder

After a recent OS update I ran into this issue.

This post along with the screen shots, saved my day and sanity! I only needed to import one folder and the rest appeared! Never needed to use EmailChemy either.

BTW — Earlier I had spoken to someone at Apple support who told me I was out of luck. So happy I listened to my gut and persisted until finding this thread.

I had the same problem where my personal mailboxes (that I had created prior to even installing El Capitan and that had been under On My Mac in Mail) just disappeared several weeks after upgrading to Sierra. I did some of what muzz63 did. I created a new mailbox under On My Mac, since On My Mac had disappeared as well. I searched in ~/Library/Mail/V4 and found all my mailboxes I had previously created in a folder in V4. (FYI to find ~/Library/Mail, open Finder, click on Go, click on Go to Folder, type in ~/Library/Mail.) I also had a V2 folder but there really wan't anything in it. There was no V3 folder. Since I now knew were my mailboxes were in the V4 folder, I noted the long name of that folder (it consists of letters and numbers - example: FFD2538B-3FCC-4194-9195-A1D3F3D28075[boat.mbox] with boat.mbox being the name of the mailbox). I skipped all the part that muzz63 did of opening the Time Machine from Finder, dragging the smallest file from the backup of El Capitan, etc. From finding out the file name in ~/Library/Mail/V4, I went directly to opening up Mail. I clicked on File, and then clicked on Import Mailboxes. I clicked on Apple Mail, clicked on Continue. (Since you hopefully just searched ~/Library, a box should open with the Library and its folders located therein, or it should be listed in Recent Places.) I scrolled down to Mail and clicked on Choose. I unchecked all the boxes except for those of the files of the mailboxes I wanted to import (example: FFD2538B-3FCC-4194-9195-A1D3F3D28075[boat.mbox], etc.), and then I clicked on Continue. All the mailboxes I imported were put in a folder called Import under On My Mac in Mail. I then just moved those mailboxes out of the folder and directly under On My Mac. Everything was back that had been there for years.

It may have been a filter was set, but when I am in Mail and go to View, there is nothing about disabling filters.

I had similar problem. But I was restoring whole system from 10.6.8 to Sierra on new MacBook Pro 2016 with TouchBar. That didn't worked for me. I had to upgrade all versions from 10.6.8. to Sierra, one by one and after 2 days a had all my local folders in Mail.

Installed Sierra (from Yosemite) on Wednesday. First noticed that my Mail signatures were gone. Called Apple Support, when first one failed, was transferred to a Senior. Repaired permissions, restored from Time Machine - still didn't work. Yesterday discovered that some of my mailbox folders were empty, some had old mail, but not recent. Another senior tech got nowhere and reported it to the Engineering Team.

I've since discovered that the missing messages are there, but they're invisible in the mailboxes. When I do a keyword search, the "invisible" messages are returned in the search results (showing as being in their proper folder), and I can read the full message from the search window. But if I open the folder, it doesn't show.

Also, messages I have read in the InBox disappear after I've read them. Demented.

Update: I think we figured it out. The tech walked me through reindexing the mail. When we launched again, there was no difference. Then I noticed under the View Menu "Disable Filter." I tried it on the InBox and it worked! On all the other folders as well. You just need to open your mailbox folders one at a time and hit Command-L to disable the filters.

I never intentionally set up filters for the mail (or Rules). It must have been some glitch or default setting in Sierra. The tech said that he had seen transition problems before with users who have a lot of nested folders. To me it's logical filing, but with younger generations, I guess they're just not into hierarchy. I hope this helps you!!

Try the demo for EmailChemy.

Select to convert Apple Mail

It will default to this location. Click Next

Convert All Messages > Convert

Save to Desktop and select Format: MBOX (standard)

When complete, find the folder that contains your local (personal) folders. The Outbox will be in Personal folders.

Example:

In Mail, Under File in the Menu bar select Import Mailboxes...

Navigate to the folder that contained your personal folders.

Import.

Check to see if these folders are visible and work correctly.

Note if this works you will need to delete the demo emails (contains a watermark) then purchase and convert again.

I had the same problem. To be clear, the folders that were missing for me were Personal folders and all were for POP accounts.

I solved it by first creating a new personal Mailbox with a distinctive name "On My Mac".

With Mail quit, next I went into the ~/Library/Mail/V4 folder and looked into the folders that had various alphanumeric names until I found the new one with the distinctive name.

I then opened up my Time Machine disc from the Finder and drilled down to the last backup from El Capitan and went to the ~/Library/Mail/V3 folder and found my previously saved personal mailboxes, and dragged the smallest one to the folder in the V4 hierarchy with the newly created mailbox in it. I just used one mailbox to test whether the process worked.

Once it had copied across I went to the ~/Library/Mail/V4/Maildata folder and deleted any file with "Envelope" in it's name.

I then restarted Mail, and got a dialog that it was importing mail and once it completed, my personal mailbox had been re-created in the macOS Sierra Mail app.

Next I repeated the above steps with all the other remaining mailboxes from my old V3 mail and once they had all copied across, deleted the "Envelope" files again. This took quite a long time as there were quite a few years worth of mail to move over but it has worked perfectly since then (as far as I can tell).

Hope that helps.

This worked for me! I can't thank you enough. I'll hang up with Apple care now. 🙂

WOW. Thank you! Worked for me too.

I had this problem collumend. Here's what I did to retrieve them but first here's a description of my problem:

• I upgraded to OS Sierra without backing up my data (at least that's what Apple geniuses told me).
• I had all my saved mail in folders "on my mac".

What I did was start over (or so I thought), so I started creating folders "on my mac" and once I created the first one, it automatically populated with the messages I had in there. It was odd, but I continued to recreate as many of the folders as I could remember, and as long as the name was the same, the computer (or the program itself) repopulated the folder with my saved message.

Why the geniuses at Apple hadn't figured this out, I don't know.

I hope this helps.