Messages In Inbox and sent mailbox have disappeared

I have been using my mac e-mail for a considerable time with no problems however in the last month, I have lost virtually all of my messages in both my inbox and sent mailbox> I have checked my preferences and the deletion of e-mails is set to 'never'. Does anyone know what might be causing this and how to stop it from happening. Thanks.

You’re welcome.
If the *.emlx files associated with those messages are gone from the filesystem, rebuilding mailboxes or re-creating the index cannot make them reappear.
There is no way to know what may have happened if you don’t know when it happened and what did you do that could have a bearing on it. What you mention about moving data between computers could certainly have a bearing on it when it happened the first time, but there is no way to know what the problem exactly was in that case either with the information you’ve provided...
If the messages are nowhere to be found and you don’t have a backup, you may try to salvage as many deleted *.emlx files as possible with a data recovery tool such as Data Rescue II, TechTool Pro, or FileSalvage. Of these, the only one I know for sure that can currently recover deleted *.emlx files is FileSalvage. Beware, however, that anything you’ve done with the computer since the messages were deleted may have caused them to be overwritten, which makes me believe your chances of recovering them now are pretty low...

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