We start with the given differential polynomials.
a1 = A1*D[p1[x, y, z], {z, 2}] -
A2*(D[p1[x, y, z], {x, 2}] + D[p1[x, y, z], {y, 2}] +
D[q1[x, y, z], {x, 1}] + D[q2[x, y, z], {y, 1}]);
a2 = A9*(A2*
D[(D[q1[x, y, z], {x, 1}] + D[q2[x, y, z], {y, 1}]), {x, 1}] +
A2*(D[q1[x, y, z], {x, 2}] + D[q1[x, y, z], {y, 2}])) -
A4*(D[p1[x, y, z], {x, 1}] + q1[x, y, z]) -
A8*D[q1[x, y, z], {z, 2}];
a3 = A9*(A6*
D[(D[q1[x, y, z], {x, 1}] + D[q1[x, y, z], {y, 1}]), {y, 1}] +
A7*(D[q2[x, y, z], {x, 2}] + D[q1[x, y, z], {y, 2}])) -
A1*(D[p1[x, y, z], {y, 1}] + q2[x, y, z]) -
A4*D[q2[x, y, z], {z, 2}];
a4 = A09*A006*
D[(D[q2[x, y, z], {x, 1}] + D[q2[x, y, z], {y, 1}]), {y, 1}] +
A004*D[q1[x, y, z], {z, 2}];
Take three prolongations (that is, derivatives with respect to each variable in turn).
diffpolys = {a1, a2, a3, a4};
vars = {x, y, z};
d2 = Join[diffpolys, Flatten[Outer[D, diffpolys, vars]]];
d3 = Union[Join[d2, Flatten[Outer[D, d2, vars]]]];
d4 = Union[Join[d3, Flatten[Outer[D, d3, vars]]]];
pvars = Cases[Variables[d4], Derivative[__][p1][__]];
qvars = Cases[Variables[d4], Derivative[__][q1 | q2][__]];
Length[d4]
(* Out[135]= 80 *)
Length[qvars]
(* Out[136]= 110 *)
110 unknowns in 80 polynomials is not promising. Undaunted, we forge ahead.
Timing[
gb = GroebnerBasis[d4, pvars, qvars,
MonomialOrder -> EliminationOrder,
CoefficientDomain -> RationalFunctions];]
(* Out[137]= {7.540000, Null} *)
So here it is.
gb
{A006*A09*A1*A4*Derivative[0, 1, 2][p1][x, y, z] +
A006*A09*A1*A8*Derivative[0, 1, 4][p1][x, y, z] -
A006*A09*A2*A4*Derivative[0, 3, 0][p1][x, y, z] +
((-A006)*A09*A2*A8 - A006*A09*A1*A2*A9)*Derivative[0, 3, 2][p1][
x, y, z] +
A006*A09*A2^2*A9*Derivative[0, 5, 0][p1][x, y, z] +
(A006*A09*A1*A4 - A004*A2*A4)*
Derivative[1, 0, 2][p1][x, y, z] +
(A006*A09*A1*A8 + A004*A1*A2*A9)*Derivative[1, 0, 4][p1][x, y,
z] - A006*A09*A2*A4*Derivative[1, 2, 0][p1][x, y, z] +
((-A006)*A09*A2*A8 - A006*A09*A1*A2*A9 - A004*A2^2*A9)*
Derivative[1, 2, 2][p1][x, y, z] + A006*A09*A2^2*A9*
Derivative[1, 4, 0][p1][x, y, z] +
((-A006)*A09*A2*A8 - 2*A006*A09*A1*A2*A9)*
Derivative[2, 1, 2][p1][x, y, z] + 3*A006*A09*A2^2*A9*
Derivative[2, 3, 0][p1][x, y, z] +
((-A006)*A09*A2*A8 - 2*A006*A09*A1*A2*A9 - A004*A2^2*A9)*
Derivative[3, 0, 2][p1][x, y, z] + 3*A006*A09*A2^2*A9*
Derivative[3, 2, 0][p1][x, y, z] + 2*A006*A09*A2^2*A9*
Derivative[4, 1, 0][p1][x, y, z] + 2*A006*A09*A2^2*A9*
Derivative[5, 0, 0][p1][x, y, z]}
This does seem to match your result. The fact that I do not understand why your method works is no indication of shortcoming (other than perhaps on my part).