You may try using Outlook client to take the backup of these public folders in a PST file and then import them on the server again using Outlook.
Steps ->
Login to a mailbox using Outlook whose mailbox is on a mailbox store which has the old PF store as default PF store. Login and take the backup of these 2 PFs in a PST.
Login to a mailbox using Outlook whose mialbox is on a mailbox store which has the new PF store as default Pf store on Mailbox store properties, put the data from PST to these folders on the server.
This should tell the system that both folders has the same data and instances should get removed from the old server.