CoW removes empty folders during import
CoW automatically leaves out empty Chrome folders when it creates your imported collection. This keeps the new Caves and Chests focused on folders that contain bookmarks or other useful organization.
Your Chrome folders remain unchanged
Import creates a copy for CoW; it never deletes or edits the folders in Chrome itself. You can create any extra Cave or Chest you want after the import.
Read how CoW imports Chrome bookmarks without losing folders.