We introduce an intrinsic Lyα emission line profile reconstruction method for high-z quasars (QSOs). This approach utilises a covariance matrix of emission line properties obtained from a large, moderate-z (2 ≤ z ≤ 2.5), high signal to noise (S/N> 15) sample of BOSS QSOs. For each QSO, we complete a Monte Carlo Markov Chain fitting of the continuum and emission line properties and perform a visual quality assessment to construct a large database of robustly fit spectra. With this dataset, we construct a covariance matrix to describe the correlations between the high ionisation emission lines Lyα, C IV, Si IV +O IV] and C III], and find it to be well approximated by an N -dimensional Gaussian distribution. This covariance matrix characterises the correlations between the line width, peak height and velocity offset from systemic while also allowing for the existence of broad and narrow line components for Lyα and C IV. We illustrate how this covariance matrix allows us to statistically characterise the intrinsic Lyα line solely from the observed spectrum redward of 1275Å. This procedure can be used to reconstruct the intrinsic Lyα line emission profile in cases where Lyα may otherwise be obscured. Applying this reconstruction method to our sample of QSOs, we recovered the Lyα line flux to within 15 per cent of the measured flux at 1205Å (1220Å) ∼ 85 (90) per cent of the time.