Hello. Would sen2three be helpful? Seems like you want cloud mask but also the resulting holes filled in. I think sen2three does this.
‘Sen2Three is a level 3 processor for the Spatio-Temporal Synthesis of bottom of atmosphere corrected Sentinel-2 level 2a images, as they are generated by the Sen2Cor application. Sen2Three takes time series of level 2a images of certain geographical areas (tiles) as input and generates a synthetic output image by replacing step by step all “bad” pixels of previous input images with the collocated “good” pixels of scenes following in time.’
http://step.esa.int/main/third-party-plugins-2/sen2three/