Proof.
Let us reformulate the statement of the proposition. Consider the category \mathcal{C} whose objects, denoted Y/X, are locally quasi-finite syntomic morphism Y \to X of locally Noetherian schemes and whose morphisms b/a : Y'/X' \to Y/X are commutative diagrams
\xymatrix{ Y' \ar[d] \ar[r]_ b & Y \ar[d] \\ X' \ar[r]^ a & X }
which induce an isomorphism of Y' with an open subscheme of X' \times _ X Y. The proposition means that for every object Y/X of \mathcal{C} we have an isomorphism c_{Y/X} : \det (\mathop{N\! L}\nolimits _{Y/X}) \to \omega _{Y/X} with c_{Y/X}(\delta (\mathop{N\! L}\nolimits _{Y/X})) = \tau _{Y/X} and for every morphism b/a : Y'/X' \to Y/X of \mathcal{C} we have b^*c_{Y/X} = c_{Y'/X'} via the identifications b^*\det (\mathop{N\! L}\nolimits _{Y/X}) = \det (\mathop{N\! L}\nolimits _{Y'/X'}) and b^*\omega _{Y/X} = \omega _{Y'/X'} described above.
Given Y/X in \mathcal{C} and y \in Y we can find an affine open V \subset Y and U \subset X with f(V) \subset U such that there exists some isomorphism
\det (\mathop{N\! L}\nolimits _{Y/X})|_ V \longrightarrow \omega _{Y/X}|_ V
mapping \delta (\mathop{N\! L}\nolimits _{Y/X})|_ V to \tau _{Y/X}|_ V. This follows from picking affine opens as in Lemma 49.10.1 part (5), the affine local description of \delta (\mathop{N\! L}\nolimits _{Y/X}) in Remark 49.13.1, and Lemma 49.12.4. If the annihilator of the section \tau _{Y/X} is zero, then these local maps are unique and automatically glue. Hence if the annihilator of \tau _{Y/X} is zero, then there is a unique isomorphism c_{Y/X} : \det (\mathop{N\! L}\nolimits _{Y/X}) \to \omega _{Y/X} with c_{Y/X}(\delta (\mathop{N\! L}\nolimits _{Y/X})) = \tau _{Y/X}. If b/a : Y'/X' \to Y/X is a morphism of \mathcal{C} and the annihilator of \tau _{Y'/X'} is zero as well, then b^*c_{Y/X} is the unique isomorphism c_{Y'/X'} : \det (\mathop{N\! L}\nolimits _{Y'/X'}) \to \omega _{Y'/X'} with c_{Y'/X'}(\delta (\mathop{N\! L}\nolimits _{Y'/X'})) = \tau _{Y'/X'}. This follows formally from the fact that b^*\delta (\mathop{N\! L}\nolimits _{Y/X}) = \delta (\mathop{N\! L}\nolimits _{Y'/X'}) and b^*\tau _{Y/X} = \tau _{Y'/X'}.
We can summarize the results of the previous paragraph as follows. Let \mathcal{C}_{nice} \subset \mathcal{C} denote the full subcategory of Y/X such that the annihilator of \tau _{Y/X} is zero. Then we have solved the problem on \mathcal{C}_{nice}. For Y/X in \mathcal{C}_{nice} we continue to denote c_{Y/X} the solution we've just found.
Consider morphisms
Y_1/X_1 \xleftarrow {b_1/a_1} Y/X \xrightarrow {b_2/a_2} Y_2/X_2
in \mathcal{C} such that Y_1/X_1 and Y_2/X_2 are objects of \mathcal{C}_{nice}. Claim. b_1^*c_{Y_1/X_1} = b_2^*c_{Y_2/X_2}. We will first show that the claim implies the proposition and then we will prove the claim.
Let d, n \geq 1 and consider the locally quasi-finite syntomic morphism Y_{n, d} \to X_{n, d} constructed in Example 49.10.5. Then Y_{n, d} is an irreducible regular scheme and the morphism Y_{n, d} \to X_{n, d} is locally quasi-finite syntomic and étale over a dense open, see Lemma 49.10.6. Thus \tau _{Y_{n, d}/X_{n, d}} is nonzero for example by Lemma 49.9.6. Now a nonzero section of an invertible module over an irreducible regular scheme has vanishing annihilator. Thus Y_{n, d}/X_{n, d} is an object of \mathcal{C}_{nice}.
Let Y/X be an arbitrary object of \mathcal{C}. Let y \in Y. By Lemma 49.10.7 we can find n, d \geq 1 and morphisms
Y/X \leftarrow V/U \xrightarrow {b/a} Y_{n, d}/X_{n, d}
of \mathcal{C} such that V \subset Y and U \subset X are open. Thus we can pullback the canonical morphism c_{Y_{n, d}/X_{n, d}} constructed above by b to V. The claim guarantees these local isomorphisms glue! Thus we get a well defined global isomorphism c_{Y/X} : \det (\mathop{N\! L}\nolimits _{Y/X}) \to \omega _{Y/X} with c_{Y/X}(\delta (\mathop{N\! L}\nolimits _{Y/X})) = \tau _{Y/X}. If b/a : Y'/X' \to Y/X is a morphism of \mathcal{C}, then the claim also implies that the similarly constructed map c_{Y'/X'} is the pullback by b of the locally constructed map c_{Y/X}. Thus it remains to prove the claim.
In the rest of the proof we prove the claim. We may pick a point y \in Y and prove the maps agree in an open neighbourhood of y. Thus we may replace Y_1, Y_2 by open neighbourhoods of the image of y in Y_1 and Y_2. Thus we may assume there are morphisms
Y_{n_1, d_1}/X_{n_1, d_1} \leftarrow Y_1/X_1 \quad \text{and}\quad Y_2/X_2 \rightarrow Y_{n_2, d_2}/X_{n_2, d_2}
These are morphisms of \mathcal{C}_{nice} for which we know the desired compatibilities. Thus we may replace Y_1/X_1 by Y_{n_1, d_1}/X_{n_1, d_1} and Y_2/X_2 by Y_{n_2, d_2}/X_{n_2, d_2}. This reduces us to the case that Y_1, X_1, Y_2, X_2 are of finite type over \mathbf{Z}. (The astute reader will realize that this step wouldn't have been necessary if we'd defined \mathcal{C}_{nice} to consist only of those objects Y/X with Y and X of finite type over \mathbf{Z}.)
Assume Y_1, X_1, Y_2, X_2 are of finite type over \mathbf{Z}. After replacing Y, X, Y_1, X_1, Y_2, X_2 by suitable open neighbourhoods of the image of y we may assume Y, X, Y_1, X_1, Y_2, X_2 are affine. We may write X = \mathop{\mathrm{lim}}\nolimits X_\lambda as a cofiltered limit of affine schemes of finite type over X_1 \times X_2. For each \lambda we get
Y_1 \times _{X_1} X_\lambda \quad \text{and}\quad X_\lambda \times _{X_2} Y_2
If we take limits we obtain
\mathop{\mathrm{lim}}\nolimits Y_1 \times _{X_1} X_\lambda = Y_1 \times _{X_1} X \supset Y \subset X \times _{X_2} Y_2 = \mathop{\mathrm{lim}}\nolimits X_\lambda \times _{X_2} Y_2
By Limits, Lemma 32.4.11 we can find a \lambda and opens V_{1, \lambda } \subset Y_1 \times _{X_1} X_\lambda and V_{2, \lambda } \subset X_\lambda \times _{X_2} Y_2 whose base change to X recovers Y (on both sides). After increasing \lambda we may assume there is an isomorphism V_{1, \lambda } \to V_{2, \lambda } whose base change to X is the identity on Y, see Limits, Lemma 32.10.1. Then we have the commutative diagram
\xymatrix{ & Y/X \ar[d] \ar[ld]_{b_1/a_1} \ar[rd]^{b_2/a_2} \\ Y_1/X_1 & V_{1, \lambda }/X_\lambda \ar[l] \ar[r] & Y_2/X_2 }
Thus it suffices to prove the claim for the lower row of the diagram and we reduce to the case discussed in the next paragraph.
Assume Y, X, Y_1, X_1, Y_2, X_2 are affine of finite type over \mathbf{Z}. Write X = \mathop{\mathrm{Spec}}(A), X_ i = \mathop{\mathrm{Spec}}(A_ i). The ring map A_1 \to A corresponding to X \to X_1 is of finite type and hence we may choose a surjection A_1[x_1, \ldots , x_ n] \to A. Similarly, we may choose a surjection A_2[y_1, \ldots , y_ m] \to A. Set X'_1 = \mathop{\mathrm{Spec}}(A_1[x_1, \ldots , x_ n]) and X'_2 = \mathop{\mathrm{Spec}}(A_2[y_1, \ldots , y_ m]). Set Y'_1 = Y_1 \times _{X_1} X'_1 and Y'_2 = Y_2 \times _{X_2} X'_2. We get the following diagram
Y_1/X_1 \leftarrow Y'_1/X'_1 \leftarrow Y/X \rightarrow Y'_2/X'_2 \rightarrow Y_2/X_2
Since X'_1 \to X_1 and X'_2 \to X_2 are flat, the same is true for Y'_1 \to Y_1 and Y'_2 \to Y_2. It follows easily that the annihilators of \tau _{Y'_1/X'_1} and \tau _{Y'_2/X'_2} are zero. Hence Y'_1/X'_1 and Y'_2/X'_2 are in \mathcal{C}_{nice}. Thus the outer morphisms in the displayed diagram are morphisms of \mathcal{C}_{nice} for which we know the desired compatibilities. Thus it suffices to prove the claim for Y'_1/X'_1 \leftarrow Y/X \rightarrow Y'_2/X'_2. This reduces us to the case discussed in the next paragraph.
Assume Y, X, Y_1, X_1, Y_2, X_2 are affine of finite type over \mathbf{Z} and X \to X_1 and X \to X_2 are closed immersions. Consider the open embeddings Y_1 \times _{X_1} X \supset Y \subset X \times _{X_2} Y_2. There is an open neighbourhood V \subset Y of y which is a standard open of both Y_1 \times _{X_1} X and X \times _{X_2} Y_2. This follows from Schemes, Lemma 26.11.5 applied to the scheme obtained by glueing Y_1 \times _{X_1} X and X \times _{X_2} Y_2 along Y; details omitted. Since X \times _{X_2} Y_2 is a closed subscheme of Y_2 we can find a standard open V_2 \subset Y_2 such that V_2 \times _{X_2} X = V. Similarly, we can find a standard open V_1 \subset Y_1 such that V_1 \times _{X_1} X = V. After replacing Y, Y_1, Y_2 by V, V_1, V_2 we reduce to the case discussed in the next paragraph.
Assume Y, X, Y_1, X_1, Y_2, X_2 are affine of finite type over \mathbf{Z} and X \to X_1 and X \to X_2 are closed immersions and Y_1 \times _{X_1} X = Y = X \times _{X_2} Y_2. Write X = \mathop{\mathrm{Spec}}(A), X_ i = \mathop{\mathrm{Spec}}(A_ i), Y = \mathop{\mathrm{Spec}}(B), Y_ i = \mathop{\mathrm{Spec}}(B_ i). Then we can consider the affine schemes
X' = \mathop{\mathrm{Spec}}(A_1 \times _ A A_2) = \mathop{\mathrm{Spec}}(A') \quad \text{and}\quad Y' = \mathop{\mathrm{Spec}}(B_1 \times _ B B_2) = \mathop{\mathrm{Spec}}(B')
Observe that X' = X_1 \amalg _ X X_2 and Y' = Y_1 \amalg _ Y Y_2, see More on Morphisms, Lemma 37.14.1. By More on Algebra, Lemma 15.5.1 the rings A' and B' are of finite type over \mathbf{Z}. By More on Algebra, Lemma 15.6.4 we have B' \otimes _ A A_1 = B_1 and B' \times _ A A_2 = B_2. In particular a fibre of Y' \to X' over a point of X' = X_1 \amalg _ X X_2 is always equal to either a fibre of Y_1 \to X_1 or a fibre of Y_2 \to X_2. By More on Algebra, Lemma 15.6.8 the ring map A' \to B' is flat. Thus by Lemma 49.10.1 part (3) we conclude that Y'/X' is an object of \mathcal{C}. Consider now the commutative diagram
\xymatrix{ & Y/X \ar[ld]_{b_1/a_1} \ar[rd]^{b_2/a_2} \\ Y_1/X_1 \ar[rd] & & Y_2/X_2 \ar[ld] \\ & Y'/X' }
Now we would be done if Y'/X' is an object of \mathcal{C}_{nice}. Namely, then pulling back c_{Y'/X'} around the two sides of the square, we would obtain the desired conclusion. Now, in fact, it is true that Y'/X' is an object of \mathcal{C}_{nice}1. But it is amusing to note that we don't even need this. Namely, the arguments above show that, after possibly shrinking all of the schemes X, Y, X_1, Y_1, X_2, Y_2, X', Y' we can find some n, d \geq 1, and extend the diagram like so:
\xymatrix{ & Y/X \ar[ld]_{b_1/a_1} \ar[rd]^{b_2/a_2} \\ Y_1/X_1 \ar[rd] & & Y_2/X_2 \ar[ld] \\ & Y'/X' \ar[d] \\ & Y_{n, d}/X_{n, d} }
and then we can use the already given argument by pulling back from c_{Y_{n, d}/X_{n, d}}. This finishes the proof.
\square
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