Every time I reload a project the last set of changes are lost
I have thought enough about some of the side effects I have reported which are what I suspect are several problems occurring together.
When I open a saved project, whatever my last changes were being lost. If I save the project and reopen, it will go back as if I was pushing the Ctrl+shift+z undo button. Hence my hold segments disappearing, the chroma key working "at random" and now the editor has uncut my videos.
Matt Stegner commented
I will ask some basic question: How are you saving the project when you close the application? How are you opening the saved project?
Attaching a video might be very helpful for the development team.