Is there no option such as “Second order linear” (called “Midside nodes on geometry” in PrePoMax) in Salome ? This should automatically generate second order elements by linear interpolation. FreeCAD has it for both Gmsh and Netgen and it’s indeed the best way to avoid negative jacobians: https://wiki.freecad.org/FEM_Geometry_Preparation_and_Meshing#Negative_Jacobians
Or follow the steps from here: Importing meshes from Gmsh and Salome_Meca
Well, Nlgeom should get rid of it.