I'm glad that at least part of your aggravation was alleviated. If you work for a long time in Shape without saving a draft or publishing your model again, you can be logged out unexpectedly. It used to happen to me all the time. Then I learned that (just as in most programs) the Save function serves the useful purpose of creating a copy of your recent work on your hard drive.
If you crash you should be able to open Shape and it should give you the option to open the automatically saved draft. If you say "No", then your work will indeed be lost.
If it gives you an unexpected error when you do publish then manually use the "Save" to create a copy, then close Shape, re-open it and you should have your saved copy available.
The "Publish As" is very useful, since it allows you to create new versions of a model. Changing the name does not create a new model - you must use "Publish As". Shape will also create multiple models with the same name. You can change the name of the model right right on the model page - just click the name and you can change it there or you can "Edit>Edit Attributes" and change it there.
To create your multiple, but nearly identical models, open the first model, make your changes, then use "Publish As". To make a second variation open the original, make your changes and use "Publish As" again.
Shape does do things a little differently, but I find that to be true of most programs. Switching back and forth from program to program as often as I do reminds me of this regularly. I hope you have better results as you work with the quirks.