This paper proposes a modification of the subspace correlation cost function and the Recursively Applied and Projected Multiple Signal Classification (RAP-MUSIC) method for electroencephalography (EEG) source analysis in epilepsy. This enables to reconstruct neural source locations and orientations that are less degraded due to the uncertain knowledge of the head conductivity values. An extended linear forward model is used in the subspace correlation cost function that incorporates the sensitivity of the EEG potentials to the uncertain conductivity value parameter. More specifically, the principal vector of the subspace correlation function is used to provide relevant information for solving the EEG inverse problems. A simulation study is carried out on a simplified spherical head model with uncertain skull to soft tissue conductivity ratio. Results show an improvement in the reconstruction accuracy of source parameters compared to traditional methodology, when using conductivity ratio values that are different from the actual conductivity ratio.