Yes, the overburden is based on the pressure with the surcharge. You are looking at the soils under the condition they are currently in.
You are basically trying to establish the relationship between the measured preconsolidation pressure (from the current test), the existing overburden pressure (with the surcharge fill), and the proposed pressure on the soil (surcharge removed, building foundation (?) added).
From there you can perform settlement calculations and determine if the settlement is within tolerable limits. Be mindful of where you obtain the sample, as BigH has said.