The Hub does automatically stop deletion of anything with a dependency usage. But that dependency usage has to be recorded on the Hub. There's no way for us to know about someone's random VAR out there in the wild.
Sometimes though, if a piece of content is in strict violation (offensive content, pirated content, etc) then it may have to be deleted regardless. In those cases, we individually notify the authors who use the dependency. I do see, however, that those authors may not have been notified for this resource in particular.
Since the authors were not notified, and since we will be relaxing the rules soon, I have restored the dependency file on the server so that those scenes will no longer be missing a dependency.