Mushrooms are a known aquaria pest, unfortunately. I have read of people replacing LR just to combat/erradicate them. I know others have use similar tactics to how you would battle aiptasia (kalk paste injections, boiling freshwater injections, etc). Manual removal also works, but becareful as cutting some 'shrroms underwater can release a toxin. I recall a thread some time ago where a reefer had to cut out a 'shroom and the next morning a nearby SPS RTNed overnight. Some people also cook their rocks to rid themselves of the mushrooms, but that is almost as extreme as flat out replacing the rock.
Best of luck in trying to rid yourself of those pests.