Danf, another good general pointer to keep in mind, especially when you're doing a lot of "save as"s with chors or models, is to periodically click "Embed all" under the Project menu.
This is also important if you bring in a model from the libraries, because if you don't embed it in the prj, any changes you make will be to the library copy as well. I think. I could be wrong. But I've gotten into the habit of clicking "Embed all" a couple of times a day. It's sort of like rubbing a lucky horseshoe.