In Continuous Deployment: Does the production codebase's file structure completely reset?

Question

I want to have a .env file in the production codebase, but do not want it on github. So I asked my colleague to add the file through terminal access on the production server.

My colleague told me that every time we merge with main, the entire directory structure on the production server resets, so we cannot do that? Is there a work around this?

I thought even in CD the production server just does an automatic "git pull origin main".

Does anyone have any ideas?