Yes, Possible. We had one client that had .com accounts and as well .org accounts. This is what we did, not sure it is the most efficient way to do it, but it worked for us.
1) we decided the .org would be the primary,
2) created new .org accounts for people that did not have .org accounts but did have .com. When done, all users from both domains should have .org accounts
3) log into each .org user account
4) go to settings, Connectivity, Email Retrieval
5) Create a new IMAP (NOT pop) retrieval task to pull all of the email from the .com account. This will also pull in sent emails, and drafts too.
6) After it completes, delete the .com account and create an alias on the .org for the .com
Accounts are essentially merged at that point.
My suggestion is to create a couple of TEST accounts with multiple levels of sub folders in the email and run the test one before you run it on everything as the folders can end up at a level you are not wanting them to be. With THIS, you can also have ALL of the mail separated into a sort of sub folder so that all of the 1st domain is maybe under a folder called "Company A", so not all emails are a straight merge of everything into the inbox. Inbox and below are Company B, Company A is the Company A Folder. So you can continue to auto filter them on the alias.
we also set up an auto responder for the .com accounts to say that the new one is a .org
If you need more details or info, let me know. Happy to help.
There is also a way to go into the folders on server for the account you want to move and rename and move the folders to the new email account, but i think it is a little more sloppy to do it that way.