Shrinkwrap feature not updating in cabling

Hello,

So recently I started implementing skrinwrap features on my skeletons for my routings on cabling. One issue I have been having is that sometimes it works perfectly when I delete a model or component from a higher level assembly and other times it just appears unusable, in other words, I try to update the skeleton (selecting automatic from manual) and the Reference tab doesn't allow me to select which body I want to delete. So here is the general process I'm following. 

Create Harness assembly -> create skel -> create shrinkwrap feature inside the skel -> grab manual bodies/surfaces -> select it as external shrinkwrap -> select manual updates -> ok

Is there anything I'm missing? Why sometimes it works as intended and sometimes it doesn't? 

Thanks and regards.