What I mean is that it's possible to embed a file into a LO document, breaking the live link between a LO file and the model. If you had done it, inadvertently, before setting up scenes, you'd be stuck with the original model without scenes.
Anyway, without sharing your file, or much more info than what you shared, we are left with guessworking. We will try guessing what might went wrong, using our experience with what we have seen before from people that did share their files and better described their issues, hoping we will help.
Silly isn't it?