Rails acts_as_paranoid and has_many :through
Well my question got down-voted, not sure why. But I found the answer:
When on a has_many through, the problem I was having was an inability to control the scope of the through model (Folders in this case).
Turns out you can just do this
@myvar = Folder.unscoped { current_user.files.with_deleted }
To whoever downvoted it - I'd like to know why, so I can ask better questions next time. Thanks!