indent offset <part of> a part

Hello all,

I am trying to create a thread to join two parts - I created it using SW2016 thread tool (so nice!), then brought that part to another and indented it.

I chucked them onto the 3D printer and let it go at it. Have now created them and realised my whoops... the threads don't run!

Basically, there's an other wall and a base part (with the insert part and indent). It created some lovely threads... unfortunately the first (outer) part needed to offset to bring the middle of the thread profile to the base of the part and now I'm trying to indent it, but I'd like to indent only the threaded part; I want the bottom face of the outer part to mate flush with the upper face of the base part, please see pictures to see what I mean:

I want to indent the threaded portion only, not the bottom face, so the upper face of the base part (highlighted blue) mates flush with the bottom face of the outer part rather than creating the gap as it is at the moment.

Thanks in advance for any help! Chris