Yup, as the others have said, the 68020 is totally disabled and doesn't execute a single instruction of the OS boot, but it depends on the nature of the damage. If it sits there and behaves like a normal disabled CPU, then it should be fine. It's quite possible though that it'll try to hold some lines low or high or something like that, meaning that the bus itself is jammed with no way for the accelerator CPU to use it.
