We present a revised version of our automated technique using Gaussian processes (GPs) to detect Damped Lyman-$alpha$ absorbers (DLAs) along quasar (QSO) sightlines. The main improvement is to allow our Gaussian process pipeline to detect multiple DLAs along a single sightline. Our DLA detections are regularised by an improved model for the absorption from the Lyman-$alpha$ forest which improves performance at high redshift. We also introduce a model for unresolved sub-DLAs which reduces mis-classifications of absorbers without detectable damping wings. We compare our results to those of two different large-scale DLA catalogues and provide a catalogue of the processed results of our Gaussian process pipeline using 158 825 Lyman-$alpha$ spectra from SDSS data release 12. We present updated estimates for the statistical properties of DLAs, including the column density distribution function (CDDF), line density ($dN/dX$), and neutral hydrogen density ($Omega_{textrm{DLA}}$).