Thanks for your input. I don't have time machine, I normally use version control via Dropbox. Not sure how Hypes auto-save works with this.
I found out that it's not actually the file itself, it's an issue with Hype. I opened the file on another Mac no problem, but then if I duplicate the same issue happens; Hype crashes on opening. Then I can't open Hype again. If I login on the same Mac with a different user I can open the file again.
The problem of moving between scenes causing a crash I worked around by duplicating the scene and deleting the offending one. The issue seemed to then affect another scene, so I followed the same procedure again and can now move between them all.
I thought the days of having to manually save different versions of a file were long gone!