TLDR: I think nUI_LeftUnitBar needs to key bind to MULTIACTIONBAR3 instead of MULTIACTIONBAR4 (and vice versa for nUI_RightUnitBar) and might be causing some of the key bind issues going on (Among other things of course). Also was wondering if you didn't assign back the "1,2,3...= keys" to ActionBar1-ActionBar= (and instead just released the bindings) if it might help that issue as well due to the fact that if these aren't listed at all in bindings-cache WoW "recreates" them.
FULL:
I've been playing around with the [ World of Warcraft > WTF > Account > {your account } bindings-cache.wtf ] file. I've found out that you can have an in combat and out of combat key set. BindingMode 0 is out of combat, BindingMode 1 is in combat. BindingMode 1 is something I've been tweaking with and if it wouldn't get overwritten when saved as 0 my keybindings would be just fine. Anyways let's look at what i have.
BINDINGMODE 0
bind BUTTON3 CLICK nUI_BottomRightBar_Button4:LeftButton
bind BUTTON4 MULTIACTIONBAR4BUTTON10
bind 1 ACTIONBUTTON1
bind 2 ACTIONBUTTON2
bind 3 ACTIONBUTTON3
bind 4 ACTIONBUTTON4
bind 5 ACTIONBUTTON5
bind 6 ACTIONBUTTON6
bind F TOGGLEAUTORUN
bind C WatchYourBack
bind SHIFT-SPACE EXAMINER_TARGET
bind ' CLICK nUI_BottomLeftBar_Button1:LeftButton
bind BUTTON5 MULTIACTIONBAR4BUTTON9
bind . CLICK nUI_BottomLeftBar_Button3:LeftButton
BINDINGMODE 1
bind BUTTON3 CLICK nUI_BottomRightBar_Button4:LeftButton
bind BUTTON4 CLICK nUI_LeftUnitBar_Button10:LeftButton
bind 1 CLICK nUI_ActionBar_Button1:LeftButton
bind 2 CLICK nUI_ActionBar_Button2:LeftButton
bind 3 CLICK nUI_ActionBar_Button3:LeftButton
bind 4 CLICK nUI_ActionBar_Button4:LeftButton
bind 5 CLICK nUI_ActionBar_Button5:LeftButton
bind 6 CLICK nUI_ActionBar_Button6:LeftButton
bind F TOGGLEAUTORUN
bind C WatchYourBack
bind SHIFT-SPACE EXAMINER_TARGET
bind ' CLICK nUI_BottomLeftBar_Button1:LeftButton
bind BUTTON5 CLICK nUI_LeftUnitBar_Button9:LeftButton
bind . CLICK nUI_BottomLeftBar_Button3:LeftButton
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The first thing I'd like to point out is LeftUnitBar and BottomLeftBar seem to save key bindings differently, I'm sure this is in the code but I don't want to go searching for this at the moment. My key binds for ' . and middle mouse button stay the same, my key binds for my two buttons on the side of my mouse go to MULTIACTIONBAR4's. When the key binding bug happens and I lose my binds I don't lose my ' . and middle mouse button but i do lose my 2 side buttons, they actually flip from using my spells on LeftUnitBar to RightUnitBar. I think the LeftUnitBar needs to save to "MULTIACTIONBAR3" instead of "MULTIACTIONBAR4" and it would fix this problem. RightUnitBar prob needs 4 instead of 3.
The second thing I notice is that if "bind 1 ACTIONBUTTON1" is left out it automatically binds 1 to AB1. If there is a way to check which button 1 through = is assigned to you could have nui make the bind 1 through = keys just null out instead of assigning 1 to AB1 and so on which perhaps might fix the error going on at the moment of 1 through = becoming unbound. After playing with it for awhile I now don't lose 1 through = as the default keybinds that I have them set up with so I'm not 100% certain with what is going on with these keys.
I hope this was of some help though after typing/reading/testing that I'm unsure if I should even post it