Some new information has come to light.
First, I must give a huge amount of credit to a tiny group of individuals who are working on the free 3DVIA Shape product. They are dedicated and working **** solving problems and meeting company goals and standards. Their schedule must match the overall Dassault Systemes schedule and DS internal product initiatives, which I can't talk about without being in real trouble.
They have fixed several bugs in the Save and Save As functions which will be in the next release. I have been burned again several times since my previous message, so I'm as eager as you are for them to be released!
Save/Save As procedures are related to how DS handles the same procedure in its many other products and the specific needs of the Shape product that changed to allow an Offline Mode. The Offline Mode has complicated the code architecture long after the core code was developed.
One suggestion that I do have that can help right now is to download and save the existing file as a 3DXML file before you make any changes. This can then be uploaded over any mistakes that might occur. It has saved my bacon several times. Working while online also helps reduce the problems that I've had.
I know that these aren't the exact answers that we want, but we are listening and moving in the right direction.