If the fork was cracked and they replaced the damaged fork, and then later found the cracked frame, you don't owe them anything.
They never should have sold you a fork for the frame you couldn't use. They never should have cut the fork to put it in a frame to test the frame. They misdiagnosed the problem, they elected to cut the fork.
If they had let you ride off and the frame broke and you got hurt, they would likely be liable, because they misdiagnosed the problem. Why should you be liable now, because they misdiagnosed the problem.
I guess you have to decide if you ever plan to do business with them again ... but there is No Way you should have to pay for a fork which you never used, and if you had used, could have caused you grave injury when the frame broke.
This is 100 percent their error. Whether or how much you want to work with them is up to you ... but you don't Owe them a thing.