Ok so I spent time refactoring to use correct masterpages. There were no multiple master pages. Spent time remaking my components. Quit Pinegrow because I was getting this error again and all my updates have gone. Seems master pages weren’t really to do with the issues.
Seems closing the project and opening it again causes the issue
In the GitHub versions, there were several master pages when I loaded the project.
Have you updated the project over there? So I can test it again with your changes?
It was still a good thing to do things properly again 
Nothing similar on my side.
Here is a branch with updated project. This has everything working and the additional dialog.
Once again, closed the project and reponed and all the work is gone. Luckily I saved this page’s HTML so can copy/paste. I’m going to check whether any other updates have been lost though harder to track as components are just more obvious. Will report back if ALL html updates have been lost.
Doesn’t seem like other HTML has been affected. Only components OR that page.
I just did a simple test of updating text on the styleguide page (outside any components), closed pinegrow, re-opened and the text is gone. Did the same text on the homepage and the text remains so it seems like it’s totally isolated to the styleguide.html page.
Another weird test, removed styleguide.html, created components.html, pasted the html from styleguide into it so we have our components. Quite Pinegrow, re-opened, components.html remains and styleguide has re-appeared!! 
@fakesamgregory
For my part, on my local WordPress setup, I’m still not experiencing the issues you mentioned. @matjaz is aware of your feedback and will also conduct investigations very soon.