While I have never tried this, I believe that if you delete the CabWriter prefix from all of the CabWriter parts you want to orphan it should work. For example, using Entity Info to rename C2LB1 Right Side to Right Side should orphan it from CabWriter. But be careful; sometimes the only thing that makes a part unique is the prefix. For example, C2LB1 Right Side and C11UB1 Right Side would be the same definition name if all you did was delete the prefix. So you might just want to use your own custom prefix. For example, C2LB1 Right Side becomes SK2LBI Right SIde or just S2LB1 Right SIde.
Greg made mention of a problem we are working on. Let me expand a little. Right now the CabWriter Production Documentation command assumes there are only the correct number of component instances in a model. However, some people might like to create exploded views by copying parts and putting them on another layer and then pulling them apart. The problem is that this would inflate the cut list and DXF files because it would include those parts copied to another layer. This week I am working on a solution that requires the user to specify a Cut List scene and a DXF scene that would have only the component instances the user wishes to include in the cut lis and dxf exports. Those scenes would include only the layers with those component instances.
This would partially solve the problem you have above, but not completely. Because, if you copied a CabWriter part to another layer and then modified it for plumbing holes for example, you would have changed the original parts. So you need to still change the prefix. Eventually, we will have this problem resolved when we are able to handle cut out etc. in version 2.0.