It's not going to damage anything else. A decoupling cap is used to filter noise from the power supplied to the component at the point where it enters the component. The only thing that might happen is that data stored in that BGA could be corrupted while writing to or reading from that BGA. If that BGA is mapped high on the memory map, then it may go unused for the most part and thus never cause a problem. If it's low in the map and is continually being used, and power to the device is noisy, then it could cause problems.
I'd say if it's working, don't worry about it.