I don't think it should because when you change the keyboard inputs and update the game, it goes over that file and resets it to the original. This can be annoying to some and it could be a problem in the future. I suggest you give two options; one is to update everything (reset the game to stock) and two is to only update the necessary files. If there are other threads similar to this or exact I'm sorry.
You could set the inputmap you don't want overwritten to "read-only" (right click... properties) or you could make a folder in the inputmaps folder called "custom" and copy your input map in there. The game is written to read inputmaps from the "custom" folder before anything else, so it should work, and you won't lose your custom inputmap on update.
I've got a quick question. I've deleted everything a while ago on the BeamNG folder except the Updater, then run the updater and let it run. The game worked perfectly but I notice I don't have a shaders folder anymore and when I run cleanup.bat it says it can't find shaders. Should I care? Or it doesn't make a difference?
there is a workaround for that: just create a folder named custom in there, put your files in there, and it *should* work.
As was already explained, in the inputmaps folder create a folder called "custom" and put custom inputmaps in there
When you say it like that, I have a folder already with my special input map in a separate folder on my desktop.