Save As vrs. Save Part As
When a part is selected, the "Save As" menu item only saves that particular part. This is not standard behavior and very unexpected, and I've come to find I'm not the only person who has lost work due to this behavior. The "Save As" command should always save the full score (parts included). A separate menu item "Save Part As" should be used to save only a part (or this could be done as part of the "Export" menu instead).
This is related to (and possibly a solution to?) the to the bug report here: https://musescore.org/en/node/272780