When the fluid is lost so is the nitrogen pressure against the seal head as the reservoir piston bottoms out. This allows the seal head, one of the two items that keeps the shock shaft centered in the shock body, free to float up and down inside the shock body. The seal head can clunk as it tops out. But now that you mention the secondary piston I guess it is possible for the seal head to stay with the secondary piston. This would reduce the centering effect on the shock shaft and may allow the piston to make contact with the bottoming cone. Not sure? But it is common to get the clunk from seal head. Guess you will find out as soon as it comes apart.