What exactly do you mean by "removed", if you've remove the textures you don't want from both "libraries" then you've broken the MAT part of the combined CMP, in the mesh are material assignments and when they can't find the textures the whole model becomes invisible in FL.
Removing the actual parts of the mesh isn't possible as it's stored under the VMeshLibrary node, 1 mesh for each LOD, the 3db parts of a CMP are what are known as "rigging" and only tell FL which vertices belong to which part, they don't hold any part of the mesh. Delete all of the 3db's and it still works in HARDCMP but FL won't use it (been there, seen it, bought the tee-shirt etc) as the instructions on how to use it are now missing, HARDCMP is no where near as fussy as FL, so just because you can see it in HARDCMP don't expect it to work in FL.
**shuffles off with a new headache**