Do you mean that the bone is flexible or that the sides of the casque are soft?
Can you post some pictures please....of the casque and the chameleon (side view)?
Does she show any signs of MBD such as what looks like an extra elbow above the real elbow, inability to lift her body off the branches, inability to shoot her tongue out far, bends to the legs or arms, etc.?
Is your chameleon getting UVB from either a tube/linear UVB light of from direct sunlight? (Neither should pass through glass or plastic.)
What brands of supplements are you dusting with and how often?
What are you feeding your insects? Do you gutload them?
What is the temperature in the basking area and what do you use for a basking light?