Q: Emails disappeared when moving them from "my Mac" to "iCloud" in Mail

Hello chriswholikesfridays,

Thanks for using Apple Support Communities. 

Based on your post, I see that while transferring emails from the On My Mac folder to iCloud, the connection was interrupted and only 100 emails were transferred. As a result, 2200 emails have disappeared from the On My Mac folder on your Mac. I do know how important it is to make sure that all of your emails are set up how you want and can be accessed. I'll be more than happy to assist you with this. 

First, I would like you to try a mailbox rebuild on the On My Mac email folder. Use Mail (Yosemite): Rebuild mailboxes, specifically, this section: 

You may need to rebuild a mailbox to update the list of messages it contains. For example, if messages appear to be missing or garbled, or if you can’t find all relevant messages when you search using the Entire Message search option. 

Select a mailbox in the Mail sidebar, then choose Mailbox > Rebuild. 

When you rebuild mailboxes for IMAP or Exchange accounts, locally stored messages and attachments are discarded, and the messages and attachments are downloaded again from the mail server to your Mac. Your mailbox appears empty until the download is complete.

Next, if you still have an issue with the emails appearing, and your email address is using Internet Message Access Protocol (IMAP), you can remove the mail account in the Mail app and then add the account. IMAP stores email messages on your Email Service Provider's server. I would advise to contact your Email Service Provider first and make sure your email is set up as an IMAP account before removing. This site will also help determine if it is IMAP: Mail Settings Lookup 

When you add the account, it should add all of your saved messages. Use Mail (Yosemite): Set up Mail with your email accounts, to remove and add an email account, specifically, these sections: 

Remove an account

When you remove an email account from Mail, the account’s messages are deleted and no longer available on your Mac. Copies of messages remain on the account’s mail server and are still available (from webmail, for example).

Important:   If you’re unsure whether messages you want to keep are still on the mail server, move or copy them into a mailbox stored on your Mac (the mailbox appears in the On my Mac section in the Mail sidebar) before you delete the account in Mail.

1. Choose Mail > Preferences, then click Accounts.

2. Select an account, then click Remove .

 

Add an account

The first time you open Mail, it may prompt you to add an email account (if you haven’t yet done so). Select an account type, then enter your account information.

To add another account, choose Mail > Add Account, select an account type, then enter your account information. Make sure the Mail checkbox is selected for the account.

If you already use an account on your Mac with other apps, such as Notes or Messages, you can also use the account with Mail. Choose Mail > Accounts to open Internet Accounts preferences, select the account on the left, then select the Mail checkbox on the right.

And finally, if you have a Time Machine backup of your Mac's data, you can restore these emails from a backup. Use the article Use Time Machine to back up or restore your Mac, specifically, this section: 

Restore from a Time Machine backup

Restore specific files:

1. Choose Enter Time Machine from the Time Machine menu , or click Time Machine in the Dock.
   
2. Find the files to restore: 
    
   • Use the timeline on the edge of the screen to see the files in your Time Machine backup as they were at that date and time. The timeline may also include local snapshots.
    
   • Use the onscreen up and down arrows to jump to the last time the contents of the window changed. You can also use the search field in a window to find a file, then move through time while focused on changes to that file.
    
   • Select a file and press Space Bar to preview the file and make sure it's the one you want. 
3. Click Restore to restore the selected file, or Control-click the file for other options.

Restore everything:

• To restore everything in your Time Machine backup, use OS X Recovery.
• To copy the files, settings, and OS X user accounts in your backup to another Mac, use Migration Assistant.

Best Regards.