Often it'll click and sometimes it'll spin down if the ROM code doesn't match. It mostly depends on headmap, micro jogs, and SA SPT. If those are all within tolerance, it'll likely just keep spinning silently. But, if one is off it'll act like it's bad heads.
As long as the SPT is the same, and the headmap of the donor ROM doesn't have extra heads, you should still be able to proceed with ldr upload to read tracks.