The first time Baxter gave Shredder a "Proove of blood" = DNA of the "death of TMNT"...so he believed the turtles die!...The rest of time probably because he thinks Baxter is only a slave with fear to do nothing without his permission...after all he destroy/punished all the Baxter-body....just Shredder dosent considere Baxter is much more than a body!!! Baxter is a dangerous mind!