You need the original clieviewer to view files from the MS, and the modified "CF Clie Viewer" to view the files on the CF.
However, there's a bug (or something) that causes the original viewer to disappear when the CF viewer is present. You need to put the CF Viewer on the CF (not in the ram) in order for both of them to be shown.
You simply delete the viewer to uninstall mini's patch. The original files are in ROM so no worries.