Most likely something else happened in addition to you editing one Key Command. Tons of folks are editing both single and multiple Key Commands everyday without incident - or these forums would be overflowing with posts about it and this is the only post about it ever. I think you are confusing coincidence with cause & effect.
This is true.
I attempted to program the Zoom Vertical function by setting “Command + Scrolling Up/Down” on mouse surface (Apple Magic Mouse). That is when it happened and I noticed afterwards that the key commands were actually not deleted, but had “Command” in front of every key.
So I guess I have to give up on trying to get Vertical Zoom to work like it does the Horizontal Zoom. I don’t understand why Cubase can do one but not the other. Its a hugely efficient editing feature in Logic and since Cubase has Horizontal Zoom on the Magic Mouse/Track Pad, you’d assume Vertical Zoom would work too.