Remove Materia and add back in?

I removed Craftsman's Cunning III and IV in the second and third spot from my Chrondite Cross Pein Hammer leaving just the first slot with materia. When I went to meld something else in those slots the message I get is 'You cannot affix any more materia to this item' Why? I tried melding the original Craftstman's Cunning back in and got the same message. So I cannot even restore the item to pre-removal. Why is that?

Edit: I removed the Cross Pein Hammer, added an old item, did a few melds, then put the Cross Pein Hammer back on and now I can meld it. What???

Are you talking about regular melding or overmelding? Not all materia can be overmelded to all slots. Some ranks can only but used in normal slots or as the first overmeld.

there's no restrictions on III's and IV's but there are on VI's, VIII's and X's.