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Is there a way to rename the .css file? Because it is giving conflict in my website, when changing the name, different from the .php file there it works perfectly.

Is there a way to change the name of the .css so that it doesn't come out with the same name as the .php file?

The name of the global css files is related to the name of the project, so renaming the project file will also rename the CSS file.
Alternative, you can a site variable:

$PROJECT_CSS$

This is documented in the help.