Optimize File(s)…    ⌃O

Removes unused audio. It reads like if I have a file with 5 regions and I delete the middle 2 then a new audio file will be created that is the 3 remaining regions. This is not the case in my simple experiments.

General advice is — do not use this command — whatever savings might be achieved isn’t worth the potential of destroying the audio files in your project.

Add and delete audio files in Logic Pro — Apple Support

Logic Pro determines which (file) segments are not contained in any of the regions used in the Tracks area. These segments are deleted, and the remaining portions of the audio file are retained and aligned side-by-side in the file. The regions in the Project Audio Browser are redefined and the project is automatically saved.