Thank you for your answers.

After a few hours spent on investigations, I found source of the problem. Configuration is OK but the problem is inside CI/CD. Locally that works fine, but in the CI/CD there are two versions at once - with CRA configuration and Vite configuration. I can see my updated and new files, but all deleted files still are visible inside pipeline. Even if I've removed postcss.config.js and rest of these old configs, they are still taken from the dev branch to which I am trying to merge my changes.