Only folder contacts get those messages ( owners are folder contacts by default)
If you uncheck "folder contacts" for those users in client permissions for those folders, they can at least avoid getting flooded by the messages. THe only way to prevent them is to use the KB below and during folder migration, you'll see alot
of those.
http://support.microsoft.com/kb/265733
XADM: How to Disable Public Folder Conflict Message Notification