The RFTools Shape Card Quarry (Clearing Quarry) is missing the recipe to turn it back into the Shape Card (Quarry) in Expert Mode. The script removes the recipes to add the new recipe, but removes both. Just a simple line after the new recipe in RFTools.zs,to add it back. Unless of course it was intentionally left that way for some reason, but the recipe for the other fortune and silk touch ones to revert it back were left in.
recipes.addShaped(<rftools:shapeCardItem:2>, [[<ore:dirt>, <ore:dirt>, <ore:dirt>], [<ore:dirt>, <rftools:shapeCardItem:5>, <ore:dirt>], [<ore:dirt>, <ore:dirt>, <ore:dirt>]]);