There are two reasons for this. First, they could have been private folders. Private folders often get trashed by conversions. Second, there is a flag on each folder called "Prohibit design refresh/replace to modify." This box must be checked on design properties, or your folders will disappear. I believe there is an agent in the Notes.net Sandbox that you can run against files to see if this is checked. If not, it will fix the issue for you.
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