To upgrade folders to the new Notes 6.5 Inbox design for a particular database use the -u switch for the convert task, e.g.
load convert -u mail\jbloggs.nsf * iNotes6.ntf
If your organisation ever ran early versions of Notes R5 (think it was about 5.02), then you should be aware that it’s possible that some users created folders on which the flag to Prohibit Design Refresh or Replace to Modify was not properly set.
There is information about this on the IBM support site, along with some code to scan for folders with this option incorrectly set:
If this was a problem for you, I would think you would already have noticed it. And if you currently run the UPDATE task on your mail servers, these folders will already have been deleted. Nevertheless, it might be work running the check script.