Wrong URL links on site with doubled contexts

Hello, everyone!
I'm having a strange problem

After a recent attack on my site, I've deleted all infected files and updated my MODX REVO site to the latest version 2.6.5.

I'm using Babel for multilanguage purposes and it was working fine before.

Now all the links on my site are generated like this: http://example.com/ru/ru/some-link/ OR http://example.com/kz/kz/some-link/

PHP version: 5.6.31. Configured through NGINX server

I was wondering what could be the problem here? Ready to provide all the necessary info and code

Hi,
I'm not sure what happened there before, but next points should be rechecked:
1) NGINX conf file
2)Contexts settings
3)Maybe something happened with Babel, I saw this befofe. It's settings should be rechecked too simultaneously with it's version.
4) Basic core settings, base_url and base_path values

Also if you talk about recent attack maybe some files are still corrupted so you have to b sure MODX update was clear and successful.