Folders removed during update

I am new to Lotus Notes. I enabled the design of a R5.0 mail template to the Web. Now, I want to shift all of my R5 client users to migrate to the Web and then access their mailboxes. I have updated the design using "load design." During the update, it removed some of the folders that were already created by users and left some others. Why did the folders get removed?
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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