Exchange 2003 is Exchange 2003, there is no such thing as a “legacy Exchange 2003” version. Do you mean an existing Exchange 2003 server and a newly built Exchange 2003 server? If this is the case there is of course no issue with moving public folders and mailboxes from one to the other. Use PFDAVADMIN to make the public folder move easier for you. I suggest you replicate them first before moving them off the other one altogether. Install the tool on your desktop pc, not the Exchange Server.