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You can restrict the face_lattice poset by using the subposet method to restrict the poset to elements corresponding to 0-faces, 1-faces and 2-faces as follows: if P is your polytope, you can do:

sage: PP = P.face_lattice()
sage: P2 = PP.subposet(P.faces(0)+P.faces(1)+P.faces(2))

Then, if you do the same with another polytope Q, you can then check:

sage: P2.is_isomorphic(Q2)