Im not at my computer at the moment but guessing
start a sketch in the assembly
select the sketch in the part in the feature tree
You should be ok with your cut then.. but sorry i cant test it just now
You might be able to automate it going down an assembly but not up...
if you can restructure a bit, smart components should do what you are asking. big difference would be you bring a component into the main assembly, and it adds the cut(s) and the other components.