There is an issue with Hype in which it sometimes thinks that an image is being used when it isn't. While this is extremely rare, I encountered this around a month ago. In the end I copied everything and pasted (with animations) into a new Hype project. This sorted it out. Fortunately it was not a complex project.
I don't know how to force a directory rebuild within Hype but it would be a nice option to have.