Complex sentence: On floppy disks, the original boot sector is moved to cylinder 0, head 1, sector 3, which is is the last directory sector on 360 Kb disks; the author presumably believed that it was "safe" to overwrite.
Split into simpler sentences: On floppy disks, the original boot sector is moved to cylinder 0, head 1, sector 3. Cylinder 0, head 1, sector 3 is the last directory sector on 360 Kb disks, and the author believed that it was "safe" to overwrite.