So...after lots of zooming out until my scene was just a tiny spec, I found the move tool! So yes, it does seem to be an error with exporting obj's between scenes! Would be cool to have this fixed in the future 🙂
I just noticed another thing actually, I'd been working on a rule file and changing things in my scene, but I hadn't been saving the rule file each time I clicked generate. This all usually works fine except sometimes my shapes would all go out of proportion with crazy cone shapes coming off my city. When I selected all my models and clicked generate this would then disapear, but I was wondering why this kept on occuring, and I suspect now that it's related to modifying and generating rules without saving the files. So note to self, always save rule files before generating them to avoid getting strange shapes in the scene... 🙂