The module has to be loaded in order for keybindings to be changed.
In any newly opened project the 'Keyboard Shortcuts' within the 'Editor Preferences' for the 'Blueprint Editor' do not appear until you have opened a blueprint within the project.
After closing and re-opening the 'Blueprint Editor' shortcuts are again no longer visible. The user who reported the issue on the AnswerHub also mentions this same issue occurs with other editor windows like Animation, Cascade, Blackboard, and Skeleton Tree.
I was able to reproduce this in all of the versions mentioned.
1. Open up any project within the affected versions mentioned.
2. Within the 'Editor Preferences' click on the 'Keyboard Shortcuts' section and observe how the 'Blueprint Editor' dropdown keybindings don't exist.
3. Close the preferences window.
4. Open and then close any blueprint.
5. Repeat step 2 and observe how the 'Blueprint Editor' section has appeared.
6. Close and re-open the project.
7. Repeat step 2 and notice how the options are gone again.
Head over to the existing Questions & Answers thread and let us know what's up.