The Link to Apple App and Link to Apple App if Modified statements support linking to iTunes via retained Apple Persistent IDs (PIDs). The Save & Remove Apple App PIDs menu items are convenience functions to save or remove the PIDs. The functions always assume the PIDs are kept in a UDTI named Apple App PID.
The Save PIDs function only works on tracks which are linked and immediately unlinks the tracks. This is to prevent the inadvertent overwriting of Apple application metadata when saving the tracks. If that was your intent you can relink the tracks before doing a Save. The unlinking protects the scenario where you are dragging tracks from an Apple application which has metadata in its library but little or none in the tracks.