Mailbox content disappears in Apple Mail 4.6

I have an iMac running OSX v 10.6.8 and Apple Mail v 4.6.
I have multiple email accounts in Mail, all are IMAP accounts through a third party email provider, and all are through the same provider. Everything worked just fine until recently.
Now, at random, all content from all inboxes but the first does not show. I know the content is there, as I can see it on my iPhone. Also, the mailbox message count (i.e. 35 messages/1 unread) doesn't show as empty; for example when empty it usually shows (0 messages/0 unread), this information is simply blank.
I can temporarily get my messages to show, by sending myself a blank message from one account to the hidden account, however at random they will disappear again.
The mailbox is relatively low on content, only a hundred messages or so...I've got others on my other machines with more than 14000 and no issues like this.
The OSX version cannot be upgraded due to software compatiblity issues that cannot be avoided.
Any suggestions would be very much appreciated!
James

James, try this...
Safe Boot, (holding Shift key down at bootup), run Disk Utility in Applications>Utilities, then highlight your drive, click on Repair Permissions, reboot when it completes.
(Safe boot may stay on the gray radian for a long time, let it go, it's trying to repair the Hard Drive & clear caches.)
Open Mail, highlight the affected account, in Mail's Mailbox menu item choose Rebuild, when done restart & see of it's fixed.

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Hello everybody,
I use Apple Mail (v. 3.6) with Mac OS X (Version 10.5.8) for my Google Domains email addresses.
Yesterday, all the sent messages suddenly disappeared from my Inbox in Apple Mail on the Mac (only for one account, although I run 6 accounts on Apple Mail). I therefore signed in with my username on Google Domains and discovered that the messages were still there in the "Sent" folder.
I tried to Rebuild my mailbox in Apple Mail but it didn't work.
After that, I removed and reinstalled the account in question in Apple Mail, but it got even worse and now every time I try to open Mail, it completely crashes. I get the coloured circle and nothing happens (except that the email account that I reinstalled blinks in alternatively on the Mac files side and GoogleMail side...). Eventually I have to force quite
Does anybody have an idea of what the problem could be and how I could solve it?
Many thanks in advance. Your help will be really helpful.
Clément.

Salut Clément, et un accueil chaleureux aux forums!
Not certain, but this can fix myriad Mail problems...
Safe Boot from the HD, (holding Shift key down at bootup), it will try to repair your Disk Directory while the spinning radian is happening, so let it go, run Disk Utility in Applications>Utilities, then highlight your drive, click on Repair Permissions, then move these folder & file to the Desktop.
Move this Folder to the Desktop...
/Users/YourUserName/Library/Caches/Mail/
Move this file to the Desktop...
/Users/YourUserName/Library/Mail/Envelope Index
Reboot.
If that doesn't help & you can afford to redo any Mail Rules...
Trash these files...
/Users/YourUserName/Library/Mail/... MessageRules.plist and MessageRules.plist.backup

E-mail disappeared from Apple Mail in Mavericks

Hello,
I think I experienced a bug yesterday in Apple Mail (I am running Mac OS X 10.9):
While organizing my e-mails, I made a new folder in my iCloud account in Apple Mail. Let's call it "Apple". Then I used the search function to find the e-mails (within my iCloud account) with a certain keyword (let's say "Pear") in order to transfer those e-mails to the "Apple" folder.
I dragged the first "Pear" conversation into the "Apple" folder. The conversation then disappeared briefly from the search results. At that moment I wanted to select the second "Pear" conversation, but in the meantime the first "Pear" conversation had been processed in the "Apple" folder and reappeared in the search results.
So I accidentally clicked again on the first "Pear" conversation and dragged it again to the "Apple" folder (even though it was already filed there) and at that moment the whole conversation disappeared. I did not manage to retrieve the messages from this conversation thereafter. I looked for them with Spotlight, in the trash, I restarted Apple Mail... Then I tried to rescue them from my iPhone but the disappearance had already synchronized to iCloud and deleted them from my phone as well.
As they are all recent messages I can't retrieve them from my Time Machine, as I only backup once a week. Furthermore, I was able to reproduce the behavior on other e-mails by using the search function and dragging an e-mail to its own folder again.
Can anyone else reproduce this?
And does anyone know how to proceed in order to retrieve the e-mails? They were not yet on my Time Machine as they are all very recent e-mails, but they are replies to my wedding save the date message so would like them back very much....
Thanks in advance for your help!

I'm practically Amish when it comes to this stuff so I'm limited to opening and deleting (I've got a ton of e mails in my deleted account and its not there either.
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Apple = Overrated

Has anyone found the solution to email disappearing with Apple Mail?

Hello,
I have seen quite a number of postings about email disappearing with Apple's Mail client, regardless of what account they are using (yahoo, gmail, aol, etc.). What I have noticed is that email vanishes right in front of my eyes from the folders I have created to keep my email in order. Sometimes I move a message or several and I see them in the folder for a day or two, and then a few days later they are simply gone. This happens from the sent folder too. It is random. No, they are not in the trash, or junk, or anywhere else. Doing a full search turns nothing. They are really, really gone.
Sometimes, I go to a folder and I see how in a second one or several messages disappear from the list and that is it. Never to be found again. Not even if I visit the web-based account I can retrieve them. They are gone.
The worst part is when they disappear from my sent folder immediately after they leave the outbox, so I am not sure if it sent or not, and I have to retype the whole thing again just to make sure.
This is extremely annoying, and I have seen I am not the only one to which this happens. Has anyone found a fix for this bug? Should I simply keep all my email in my inbox? Or should I just give up on Apple Mail and use Thunderbird?
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Let's see if we can dind how many Mail files on your computer.
http://validator.w3.org/
I'd get EasyFind...
http://www.macupdate.com/info.php/id/11076
Here's a direct download link to EasyFind 4.0 which runs in 10.3.9 & up...
http://www.devon-technologies.com/files/legacy/macosx1039/EasyFind.dmg.zip
From this page,
http://www.devon-technologies.com/support/faqs.php?p=default&cat=19
Freeware applications:
    * EasyFind 4.0
    * PhotoStickies 5.6
    * ThumbsUp 4.3
    * XMenu 1.8
http://www.versiontracker.com/dyn/moreinfo/macosx/8707
Use it to search your whole drive for case insensitive & show invisibles...
.emlx
(dot ee em el ex)
Find Any File...
http://apps.tempel.org/FindAnyFile/
Hold Option/alt when clicking on Find button to Find All.

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Not certain, but this can fix myriad Mail problems...
Safe Boot from the HD, (holding Shift key down at bootup), it will try to repair your Disk Directory while the spinning radian is happening, so let it go, run Disk Utility in Applications>Utilities, then highlight your drive, click on Repair Permissions, then move these folder & file to the Desktop.
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/Users/YourUserName/Library/Mail/Envelope Index
Reboot.
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/Users/YourUserName/Library/Mail/MessageRules.plist
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Mailbox content disappears in Apple Mail 4.6

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