I have had mixed success with the Export-Mailbox command in the past. In one case, I absolutely needed to perform an Export of a Mailbox and given the numerous errors and failures ended opening up a ticket with Microsoft. Their response was that the mailbox was "corrupt" and the only way to overcome this "corruption" was to move the mailbox to another store or run ESEUTIL and fix any logical corruption(not going to happen in production system).
Anyhow, I moved the mailbox and it did the trick, however, I did a bit of Investigation and Experimentation and found that in the vast majority of the cases the items in the Dumpsters were the culprit. When I run into Export-Mailbox issues, I cleanup or restore any items in the users mailbox dumpster(s) (since they are going to be restored anyways when you export) rerun the cmdlet, and in over 95% of the cases it succeeds.
Just my 2 cents on the subject and MS, pleeeeease bring Ex-Merge back!