Mail can't index after upgrading to yosemite

Question

I am on a Macbook Pro, Yosemite 10.10. 2.53 Intel Core 2, 4GB Memory.
A few weeks ago I updated to Yosemite from an older OS. All seems to be working fine, except for Apple Mail. It is having trouble indexing the mail. I did have a large storage of mail for my business and my personal. I don't know how to proceed. I did perform a backup via Time Machine.
Here's what I did:
When I try to open Mail, it says it needs to import messages. I click 'Continue'.
After about 6 or 7 minutes, it appears to be done importing my 25K messages.
I get a message saying it is upgrading my mail database and migrating my data.
Then I get 'The upgrade failed. An error occurred durig the upgrade. Click Continue to launch the Mail Import Assistant, which will help you create a new library and import your existing messages.'. I click Continue.
I get an error message saying, 'Your Mail Index has been damaged. To repair it, quit Mail. Mail will repair the index the next time you open Mail. Your mailboxes and messages will be preserved.'. This has not worked when I open Mail the next time.
I have tried to go to Migration Assistant, but that did not seem to be what I was looking for. I cannot find where my mailbox folders are stored in order to delete several folders and their contents if I have too many stored messages.
Please help. I am not sure what to try to get Mail to open and to recover my messages. Thanks.

Answer 1

The new version of Mail stores its database in a different format than the old one, so the database has to be converted before Mail can use it. Sometimes the conversion fails because the old database is corrupt. The easy way to recover is to discard the old database and start afresh. You can do that without losing any messages, provided that:
☞ All your incoming mail accounts are on an IMAP or Exchange server
☞ You store sent messages on the server
☞ You don't have any "On My Mac" mailboxes
Most well-known independent mail services such as iCloud and Gmail are based on IMAP. On the other hand, ISP-hosted mail services almost always use POP. If your ISP is one of your mail service providers (or the only one), you probably can't use this procedure. Ask for further instructions in that case.
If you know that the conditions above are satisfied, continue as follows.
Quit Mail if it's running. Back up all data.
Open the Library folder in your home folder by holding down the option key and selecting
          Go ▹ Library
from the Finder menu bar. Inside it is a subfolder named "Mail." Move that folder to the Desktop. You're not moving the Mail application; you're moving a folder named "Mail."
Open the Internet Accounts pane in System Preferences and recreate your mail accounts other than iCloud with the same settings as before. To recreate an iCloud mail account, all you have to do is open the iCloud preference pane and check the box marked Mail.
Launch Mail. If all goes well, your mailboxes should be restored automatically. The messages will be downloaded from the servers, so it may take a long time if you have very large mailboxes. Some people have mailboxes in the gigabyte range, and that may be a problem if your bandwidth usage is metered.
If the mailboxes are created successfully, you can delete the folder you moved to the Desktop. You may have to recreate your Mail rules, signatures, and custom stationery. If it's very important to you not to have to do all that, ask for instructions before deleting the folder.