It's not removing extensions, it is completely skipping loading extensions, restarting didn't helped, nor Verify files integrity from Steam.
I've just solved by making a clean installation and copied my backup over WITHOUT overwriting any original files.
No idea what's that about, I think I had a error message when it started happening but I didn't gave a good look at that, it never showed again and it started skipping all extensions.
(and no, the extensions aren't on the list of extensions to skip)
Edit: I just mentioned having to manually install every extension cause I thought one of them were corrupt.
It could be a built-in extension that triggered that, no idea, since copying my whole backup without overwritting just the original ones did worked fine.
Perhaps it could be something else, like a corrupt dll, or runtime, something... But the strange part is that these couldn't be replaced by Steam when verifying.
Edit 2: OH NO, happened again...