Thanks DI, yes I know how to do it in HX Edit, but I said NATIVE in every post.
My user defaults were wiped out from Native which are stored in the mentioned file, there is no option to backup user defaults in Native.
Everything is alright now, I manually restored most of my defaults.
Edit:
I have a small theory how that might happen.
When Helix Native is loaded it reads the #UMDStore file with all the user defaults, if for some reason Native fails to read this file is will create a new file completely blank over it if you save any new user default.
I think that's what happened to me, and I think it is very rare, probably due to my antivirus glitching and preventing Native from reading the file.