In brief: If user assigns a shortcut to a menu created by a script, the shortcut will be lost after opening the Keyboard Shortcuts window again and clicking Cancel.

A detailed description of the bug is here:
https://forums.adobeprerelease.com/indesign/discussion/2354/shortcuts-assigned-to-custom-menus-lost-after-opening-keyboard-shortcuts-again-clicking-cancel#latest

Affects both InDesign 2023 and 2024.

It appears that it only happens on Mac.