Which metadata stores custom CSS for a community?

The sad truth is, virtually the entirety of the configuration you can do in Community Builder is saved in that monolithic binary.

If you want to know whether to "trust" that the binary contains your custom CSS...

1. Spin up a sandbox.
2. Open Community Builder in the sandbox and verify what you see in the CSS.
3. Change the CSS in the sandbox.
4. Create a change set from production to sandbox containing the Community binary.
5. Deploy, and check again what you see in CSS for the sandbox.