I’ve also had this happen with footprint libraries too.
Usually adding new or deleting obsolete or absent library from Manage Symbol Library
Kicad 5.1.9 Mojave 10.14.6
I’m new to Kicad so groping around with libraries, wish I could be more specific. I apologize if this isn’t in the correct forum category.
It is better to manage a library of your own under your direct control than to try and alter the pre-installed libraries (beyond hiding ones you do not require).
The pre-installed libraries are in a portion of the drive that macOS has set as read-only.