There is nothing you can do other than to merge or change email addresses.
XenForo does not permit the same name or email address to be used for more than one user, so you will be required to confirm what to do in the case of any affected users. The options available are to merge them or rename and change the email address.
What about letting the importer automatically merge the duplicates? The merged users can still use their email to login. They can contact you directly if they wish to change the username they end up with after the merge.
The numbers are even higher, I see now that over 400 members have more than one account at the forum (we opened up for that to get more activity in the beginning). As it is now I just have to merge them and hope it goes well, and as Jake says I'll have to tell them to contact me if they want any changes to their username.