When using Save and Replace under the productivity tools the command ignores the current selection priority and uses part priority. This is extremely annoying when trying to save and replace a sub assembly. The work around is to select the assembly before clicking the command or selecting it from the model browser, neither of which come to mind until after you fail at selecting the assembly in the graphics window.
I filed a support case on this and it was judged not to be a bug, so here is a feature request to make the command respect the current selection priority.