A pic would help. From what you described you can cut the bottom dead skeleton portion. I wouldn't cut withing 2-3 inches of the heads where the living tissue is.
I predrilled my live rock to accept skinny acrylic rods. I can then drill the bottom dead portions of the hammer/frogspawn/torch skeleton. Place a rod in the 1/2 inch hole and crazy glue the acrylic rod into the skeleton. As the coral grows I can move it around within the live rock structure
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