Hi Nick - When we went live with Windchill 10 approximately 6 months ago, I have heard lot of complaints from my users on not saving the work in Pro/E. The main reason I found to cause this issue is users have not checked out the entire assembly and when they try to modify, the pop-box comes with saying "Check-out now" option and if you click OK; it sometimes fail to check out the part because somebody else might have checked out the same object. When it fails to check out the object, it also fails to save the object in Pro/E.
I am not sure above comments is the issue you are having but it could be helpful to layout the best practice document and hand out to user community.
The best practice in case above would be check out assembly with all its components OR hit "continue" while the pop box comes up and then later you can update the object in your workspace.
Contact me if you have any questions.
Jay Shah
