Don't be afraid. Repot it just like anything else. Take it out of the disgusting basket and medium. Wash off the pseudobulbs and roots removing the mushy dead ones (roots and back bulbs), treat it with whatever you usually use for killing scale, and pot it up in a fresh basket and medium. The new growths will start again from the old back bulbs - just like you are seeing now. Don't worry if the back bulbs fall apart, either. Just pot them all up in a new basket, making sure they are firm (not wobbly)
I use a finer bark in a basket lined with either sphagnum moss or other material that will keep the medium in the basket but also let the spike emerge from the bottom or sides of the basket, but some people use medium bark, or sphagnum moss. Some people like to mount these on cork. So you have a great latitude in how you want to proceed. There's no one right answer. Just kill the bugs and you're good to go. Sometimes I use an old toothbrush dipped in soapy water to help brush the scale off the back bulbs. Then spray it with 70% rubbing alcohol. There are any number of methods to kill scale. You could search this site (or google) for various methods & recipes
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