Our Sentry project is configured with a fingerprint rule. I would like to define an SDK level fingerprint for certain events. Will the SDK level fingerprint override the project level configuration, or will it merge with it?

Server side fingerprinting rules override client side SDK fingerprinting. It is not possible to use client side fingerprinting rules in place of server side rules or to combine the two. You'll have to choose either server side or client side fingerprinting.