After updating to 10.9.1, mails (for exchange) in subfolder are gone

Quit Mail. Force quit if necessary.

Back up all data. That means you know you can restore the Mail database, no matter what happens.

Triple-click anywhere in the line below on this page to select it:

~/Library/Mail/V2/MailData

Copy the selected text to the Clipboard by pressing the key combination command-C. In the Finder, select

Go ▹ Go to Folder

from the menu bar. Paste into the box that opens (command-V), then press return.

A folder window will open. Inside it there should be files with names as follows:

• Envelope Index
• ExternalUpdates.storedata

Move those files to the Desktop, leaving the window open. Other files in the folder may have longer names that begin as above. Move those files, if any, to the Trash.

Log out and log back in. Relaunch Mail. It should prompt you to re-import your messages. You may get a warning that the index is damaged and that Mail has to quit. Click OK. Warning: The process may take hours if you have gigantic mailboxes. For reasonable-sized mailboxes, it should only take a few minutes.

Test. If Mail now works as expected, you can delete the files you moved to the Desktop. Otherwise, post your results.

Configuring Mail for your email account

Mail: Exchange account messages may temporarily not appear

Using Microsoft Exchange 2007 (EWS) accounts in Mail

Please read this whole message before doing anything.

This procedure is a diagnostic test. It won’t solve your problem. Don’t be disappointed when you find that nothing has changed after you complete it.

The purpose of this test is to determine whether the problem is localized to your user account. Enable guest logins* and log in as Guest. Don't use the Safari-only “Guest User” login created by “Find My Mac.”

While logged in as Guest, you won’t have access to any of your personal files or settings. Applications will behave as if you were running them for the first time. Don’t be alarmed by this; it’s normal. If you need any passwords or other personal data in order to complete the test, memorize, print, or write them down before you begin.

Test while logged in as Guest. Same problem?

After testing, log out of the guest account and, in your own account, disable it if you wish. Any files you created in the guest account will be deleted automatically when you log out of it.

*Note: If you’ve activated “Find My Mac” or FileVault in OS X 10.7 or later, then you can’t enable the Guest account. The "Guest User" login created by "Find My Mac" is not the same. Create a new account in which to test, and delete it, including its home folder, after testing.

Do you use two step verification for your exchange account, if you do you will need to create an app password. If you don't know what that is you probably don't use it. Can you get mail on the actual website?

Delete the account from the mail app and add it back again.

Back up all data.

Select all your mailboxes, and then select

Mailbox ▹ Export Mailbox...

from the Mail menu bar. Export the mailboxes to the Desktop folder.

Make a note of the settings for all your Mail accounts – everything you'd need to reconstruct the settings from scratch.

Quit Mail. Then select

 ▹ Force Quit...

from the menu bar. A small window will open with a list of running applications. Mail may appear in that list, even though you quit it. If so, select it and press return. Close the window.

In the Finder, hold down the option key and select

Go ▹ Library

from the menu bar. Move the following items from the folder that opens to the Trash (some may not exist):

• Caches/com.apple.mail
• Saved Application State/com.apple.mail.savedState

Leave the Finder window open for now.

Relaunch Mail and test. If the problem is solved, you’re done. Delete the exported mailboxes. Otherwise, quit Mail and move these items, if they exist, from the open Library folder to the Desktop:

• Application Support/AddressBook/MailRecents-v4.abcdmr
• Containers/com.apple.mail
• Mail
• Preferences/com.apple.mail.plist (OS X 10.7 only)
• Preferences/com.apple.mail.searchhistory.plist (OS X 10.7 only)

Note: you are not moving the Mail application. You’re moving a folder named “Mail.”

Log out and log back in. Launch Mail. It will behave as if you were setting it up for the first time. Go through the setup process with one of your accounts, using the information you noted earlier. Test. Same problem?

If there’s no improvement, quit Mail again and put back the items you moved to the Desktop, replacing any newer ones that may have been created in their place. You don’t need to replace the items you moved to the Trash.

If the issue is resolved, recreate the rest of your Mail settings, then import the mailboxes you exported:

File ▹ Import Mailbox...

After importing, test. If Mail is still working, delete the items on the Desktop and close the Finder window.

I am having some issues as well. After updating to 10.9.1 None of my mail accounts can connect. When I open connection doctor it says:

"Could not connect to this iCloud IMAP server. Check your network connection and that you entered the correct information in teh Accounts preferences. Also verfiy that your server supports SSL. If it does not, deselect "Use SSl" checkbox in the advanced tab of Account preferences."

All of the accounts worked fine BEFORE i updated. Also, iMessage accounts can no longer connect either.

When i check SOftware update it says it installed 10.9.1 OSX update TWICE yesterday. My guess is that is the culprit. I tried resetting mail like suggested above, but still no connection.

Is there any way to un-instal an OSX update or to install a previous version? Unfortunately i do not have a system backup....