If you are getting this warning for the user it means that the folder ID for Notes has changed. In this users mailbox every folder has an ID and they should never change.
The BES will only sync the defualt folders, Contacts/Calendar/Notes/Tasks. Right now to the BES the Notes folder looks like it was deleted and re-created and the BES will not sync this folder any more because of that.
There is an article from RIM on how to check the folder ID to see if it did indeed change: BlackBerry Search Results
If so the work arounds are:
1. Turn off wireless sync for the affected folder and then activate
2. Re-create the mailbox
I'm sure there are others but I wouldn't want to risk ruining a mailbox. I also believe that Microsoft is looking into this as well because they don't know why the ID changes either.
Hope this helps.