Had same problem. Mortar stains on glass for a year +. Removed the mortar with regular stanley blade mositened (careful use of stanley to avoid scratching) but the horrible etch marks remained. Very prominent when the sun shined. Spoke to my window supplier and he advocated very gentle rubbing of affected areas with fine steel wool. Spent some time doing this (again wet panes first) and its made a huge improvement. Etch stains are barely visible now. Maybe worth a try.