How to transfer mailboxes (V3 file) on El Capitan

I have two iMacs, one in home office (main computer) and one in company office (secondary computer). Once a week, I transfer all of my mailboxes (along with all email messages contained therein) from my main computer to my secondary computer.

When both were running Mavericks or Yosemite, all I had to do was copy the V2 file in ~/Library/Mail from my main computer to the secondary computer, and all email messages transferred successfully. When I upgraded both iMacs to El Capitan, I noticed that all the mailboxes are now in V3 file in ~/Library/Mail, so I transferred the V3 file from my main computer to the secondary computer. However, after the transfer, none of the mailboxes on the secondary computer contained any messages any longer. I cannot seem to be able to transfer V3 file under El Capitan in the same way that I used to transfer V2 file under Mavericks/Yosemite.

What am I missing? How am I supposed to transfer V3 files (or all existing mailboxes and messages) from one Mac to another under El Capitan?

Any help or suggestion will be appreciated. Thank you so much.

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I have found a solution by myself. For anyone else who might be having the same problem, all you have to do is rebuild each mailbox, after you restart Mail (after the transfer of the V3 file). All the messages are there, but they don't show up within each mailbox until it is rebuilt. It is cumbersome if you have hundreds of mailboxes (as I do), but it is possible to select several mailboxes and rebuild them all simultaneously.

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