Basically what I said before, saw this when testing Htt on various sites. You
want all project folders and their HTT files in the same root folder. Then
open HTT and open a project file in the root folder, then exit out. It should
update the index file in the root folder.
Example
Archived Sites (Folder)
  Website 1 (Folder)
  Website 3 (Folder)
  Website 2 (Folder)
  Website 1.whtt (file)
  Website 2.whtt (file)
  Website 3.whtt (file)