be sure that u’re working with the geometry, not preview adaptive mesh u usually obtain pressing a.
u have to hit make adaptive skin, that way, z b creates real geometry as a tool in tools panel.so what u have on the screen still is the preview one
then clear the layer, (ctrl+n)
then select the right tool, wich lists in its infos not z spheres, but polygons number only. drag the tool into screen , then press t go into edit mode and x to work in simmetry mode as well.just as u di when u first draw your z sphere.
u will get your delete hidden only with real geometry.
after hiding eyes polys BTW.