One common method to determine heat flow in a well is to use a Bullard plot, which graphs thermal resistance (m$^2$K W$^{-1}$) against temperature. The gradient of this line is heat flow, and the uncertainty determined from the error of linear regression.
Thermal resistance is calculated by:
$$ R = \sum_{i=0}^{n} \left( \frac{\Delta z_i}{k_i} \right) $$
which is the cumulative summation of resistors down the length of a borehole. The uncertainty on $R$ should increase as the individual errors on $k$ accumulate.

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