switching regulator output filtering
My question is where should the V_sense resistors connect, before or
  after the secondary LC filter?


It should almost certainly NOT go after the 2nd LC filter because you'll turn the circuit into a power oscillator.

With feedback systems you have to take care of not introducing too much phase shift or delay or negative feedback (desirable) becomes positive feedback (turns into an oscillator).

The regular LC filter in a switcher introduces anything up to 180 degrees of shift and this is compensated by good chip design and compensation component selection. See this: -

9.2.2.6 Compensation Components

and this: -


  8.3.7 
  
  Slope Compensation In order to prevent the sub-harmonic oscillations
  when operating the device at duty cycles greater than
  50%, the TPS54531 device adds a built-in slope compensation which is a
  compensating ramp to the switch-current signal.


Note the parts about slope compensation. Adding another LC network within the feedback loop is asking for trouble.