Matt already addressed your main challenge, but I thought it might be helpful to add one more tip. You say:

"If I delete the WIKI section from the folder, then re-attach "another" one, it ends up with the same pages."

In other words, you expect all wiki pages for a folder to be deleted when you close the webpart (aka "WIKI section") displaying them on a folder portal page. Not an unreasonable expectation.

Actually, your wiki pages are purposefully retained when you close/delete a wiki webpart. Britt gave me a great explanation for this behavior:

"Webparts are just windows onto underlying data- deleting a webpart will never delete actual data. That is, after deleting a webpart, you can always add the webpart again, and you'll see the pre-deletion data, assuming that the webparts have the same settings. "