Can an FIR be quashed if both parties have reached a compromise in a non-compoundable case?

Yes. The High Court under Section 528 BNSS (482 CrPC) has inherent powers to quash non-compoundable FIRs (such as matrimonial disputes, private commercial quarrels, or minor physical altercations) if parties have amicably settled and continued prosecution would be an abuse of process (Gian Singh v. State of Punjab).