I actually think I may have had the same problem, where the game didn't want to unbind those from in-game.
But I use a full-on custom route of setting up my keybinds. Create the files that don't exist (use notepad, and set proper extensions where needed)
(1. in-game)
Keyboards/eq2_keymap_custom.ini:
Set your keys up in-game and then save them with
/save_keymaps eq2_keymap_custom.ini
Now log out and close the game
(2. edit)
eq2_recent.ini:
Code:
cl_configuration_file EQ2-CustomMode.cfg
(3. file create)
Layouts/EQ2-CustomMode.cfg:
Code:
name=Custom
options=
uisettings=
colors=
keymaps=eq2_keymap_custom.ini
This will make your keyboard layout show up in the in-game options menu dropdown, too.
With this route you can be sure that your options will save, and you can setup custom colors.
BUT BE AWARE OF WHEN SONY ADDS NEW KEYS, because they will be blank by default when they do

(example: flying mounts control keys, or inventory+persona window merged into character window. Just need to edit keys in options and re-save Step 1)