Will updating macOS delete my kext configuration I have after disabling discrete GPU permanently from EFI? I have followed all the instructions provided at MacBook Pro: How to disable discrete GPU permanently from EFI? 

My question is:

Is it safe to update my macOS to latest High Sierra or even to Mojave (Recently I have High Sierra 10.13.1) or it will erase all my kext settings and make my broken GPU appear again? And do I have to do all the process all over again from the beginning, which I would like highly to avoid.

Sorry if this question been asked before, since i cant find this question somewhere else.
As it's currently written I have to assume that you followed the highest voted answer. That means you only removed the dGPU kexts. That is suboptimal anyway. 

Look here for a better solution.

https://apple.stackexchange.com/a/295805/251859



Now, updating macOS 10.13.1 to 10.13.5 will install a non-working but critical kext (AMDRadeonX3000.kext), thereby your machine will still boot.

That changes with 10.13.6, where a working, new kext will be installed. That means you will then have to move the kext again.  

On upgrading to Mojave you will naturally get a full set of working kernel extensions. If that is coupled with a non-working dGPU that will lead to a boot failure. This requires additional operations then.

But that shouldn't bother you much, as most MacBook Pros for which that hack is intended are not officially supported b Mojave. That means it is unlikely that you upgrade by accident through a wrong click in the AppStore…