Start with a blank slate, wipe out all collections. Make a directory and put 3 pictures in it. In the viewer, mark all 3 pictures. Check that they've shown up in coll://Marked Pictures. Exit all dopus. At the command prompt, execute:
dopusrt.exe /col clear "Marked Pictures"
Run dopus. Navigate to coll://Marked Pictures and notice it is now empty. Go back to the pictures you had marked and view them. Cycle through them all and notice they are marked.
Navigate back to coll://Marked Pictures and confirm it still shows as empty.
This bug does not impact delete as /col delete "Marked Pictures" works just fine and gives expected behavior.
There is a problem there but I think it is just that "clear" removes the sub-collections from "Marked Pictures" so they don't appear to be there (but they still exist if you navigate to them directly, or check the config files on disk).
If you want to remove all the collections below Marked Pictures, delete is the way to go. I don't think it would make sense for clear to be recursive (except possibly as a separate option). But there is a bug here where the sub-collections are removed from the parent but still exist, definitely.