A ability to preserve layer and table IDs between map service updates is a great feature added at 10.3.1. Unfortunately it seems that it has to be manually applied to each dataframe when an .mxd is created.
Map publishers rarely remember to enable it and I occasionally end up having to edit my applications after updates anyway.
Allowing ArcMap to be configured to allow dataframes have this option turned on by default would greating enhance the usefulness of this feature.