the easier way it's the declaration of any transformation to be done, via pattern matching, and a generic rule working recursively on any pattern:
% specialize for VP
transfer(vp(X,Y), vp(V,U)) :- !,
transfer(X,U), transfer(Y,V).
% generic rule, work out arguments
transfer(X, Y) :-
X =.. [F|Xs],
maplist(transfer, Xs, Ys),
Y =.. [F|Ys].
If you need your program to be able to work bidirectionally, check the variables instantiation in generic rule
transfer(X, Y) :-
nonvar(X), !, X =.. [F|Xs],
maplist(transfer, Xs, Ys),
Y =.. [F|Ys].
transfer(X, Y) :-
Y =.. [F|Ys],
maplist(transfer, Xs, Ys),
X =.. [F|Xs].
yields (for instance)
?- transfer(s(np(n(he)), vp( v(went), np(adj(his), n(home)))),T2).
T2 = s(np(n(he)), vp(np(adj(his), n(home)), v(went))).
?- transfer(T1,$T2).
T1 = s(np(n(he)), vp(v(went), np(adj(his), n(home)))).