cloning particular subfolders

 I need to merge two drives into a third one.  Can I clone an old HDD to a new SSD, including all 118 subfolders of Outlook 2003, and   add/clone just some specific Outlook 2010 subfolders from the second "old" drive? Will there be a conflict, e.g. the Outlook2010 mails won't be accepted/allowed by 2003? I would like to keep the 2003 as default.