Jamie, I am confused a bit by this discussion.
If the Save Anyway button is selected, the Leave / Cancel message is shown. If the Cancel is selected, you are stuck in a loop on the page, but I thought that 'you' had said that the changes were already saved at that point.
I have made a very minor change on Davis-13707 to remove the last item in the Sources section 'Ancestry Tree, no id'. I selected the 'Full Save', then selected 'Save Anyway', then the 'Leave or Cancel' message is shown. Without selecting either option, I opened the same profile up in a different browser. The 'save' has not been done to the profile. The last item still exists in the profile, so it looks like the profile is not being saved until the 'Leave' is selected.
I did this in FF, so it was a different browser than Chrome.