Proof.
Let U \subset X be affine open. Looking at Topologies, Definitions 34.8.4 and 34.10.7 it suffices to show that the base change \{ X_ i \times _ X U \to U\} can be refined by a standard ph covering if and only if it can be refined by a standard V covering. Thus we may assume X is affine and we have to show \{ X_ i \to X\} can be refined by a standard ph covering if and only if it can be refined by a standard V covering. Since a standard ph covering is a standard V covering, see Topologies, Lemma 34.10.3 it suffices to prove the other implication.
Assume X is affine and assume \{ f_ i : X_ i \to X\} _{i \in I} can be refined by a standard V covering \{ g_ j : Y_ j \to X\} _{j = 1, \ldots , m}. For each j choose an i_ j and a morphism h_ j : Y_ j \to X_{i_ j} such that g_ j = f_{i_ j} \circ h_ j. Since Y_ j is affine hence quasi-compact, for each j we can find finitely many affine opens U_{j, k} \subset X_{i_ j} such that \mathop{\mathrm{Im}}(h_ j) \subset \bigcup U_{j, k}. Then \{ U_{j, k} \to X\} _{j, k} refines \{ X_ i \to X\} and is a standard V covering (as it is a finite family of morphisms of affines and it inherits the lifting property for valuation rings from the corresponding property of \{ Y_ j \to X\} ). Thus we reduce to the case discussed in the next paragraph.
Assume \{ f_ i : X_ i \to X\} _{i = 1, \ldots , n} is a standard V covering with f_ i of finite presentation. We have to show that \{ X_ i \to X\} can be refined by a standard ph covering. Choose a generic flatness stratification
X = S \supset S_0 \supset S_1 \supset \ldots \supset S_ t = \emptyset
as in More on Morphisms, Lemma 37.54.2 for the finitely presented morphism
\coprod \nolimits _{i = 1, \ldots , n} f_ i : \coprod \nolimits _{i = 1, \ldots , n} X_ i \longrightarrow X
of affines. We are going to use all the properties of the stratification without further mention. By construction the base change of each f_ i to U_ k = S_ k \setminus S_{k + 1} is flat. Denote Y_ k the scheme theoretic closure of U_ k in S_ k. Since U_ k \to S_ k is a quasi-compact open immersion (see Properties, Lemma 28.24.1), we see that U_ k \subset Y_ k is a quasi-compact dense (and scheme theoretically dense) open immersion, see Morphisms, Lemma 29.6.3. The morphism \coprod _{k = 0, \ldots , t - 1} Y_ k \to X is finite surjective, hence \{ Y_ k \to X\} is a standard ph covering and hence a standard V covering (see above). By the transitivity property of standard V coverings (Topologies, Lemma 34.10.5) it suffices to show that the pullback of the covering \{ X_ i \to X\} to each Y_ k can be refined by a standard V covering. This reduces us to the case described in the next paragraph.
Assume \{ f_ i : X_ i \to X\} _{i = 1, \ldots , n} is a standard V covering with f_ i of finite presentation and there is a dense quasi-compact open U \subset X such that X_ i \times _ X U \to U is flat. By Theorem 38.30.7 there is a U-admissible blowup X' \to X such that the strict transform f'_ i : X'_ i \to X' of f_ i is flat. Observe that the projective (hence closed) morphism X' \to X is surjective as U \subset X is dense and as U is identified with an open of X'. After replacing X' by a further U-admissible blowup if necessary, we may also assume U \subset X' is scheme theoretically dense (see Remark 38.30.1). Hence for every point x \in X' there is a valuation ring V and a morphism g : \mathop{\mathrm{Spec}}(V) \to X' such that the generic point of \mathop{\mathrm{Spec}}(V) maps into U and the closed point of \mathop{\mathrm{Spec}}(V) maps to x, see Morphisms, Lemma 29.6.5. Since \{ X_ i \to X\} is a standard V covering, we can choose an extension of valuation rings V \subset W, an index i, and a morphism \mathop{\mathrm{Spec}}(W) \to X_ i such that the diagram
\xymatrix{ \mathop{\mathrm{Spec}}(W) \ar[d] \ar[rr] & & X_ i \ar[d] \\ \mathop{\mathrm{Spec}}(V) \ar[r] & X' \ar[r] & X }
is commutative. Since X'_ i \subset X' \times _ X X_ i is a closed subscheme containing the open U \times _ X X_ i, since \mathop{\mathrm{Spec}}(W) is an integral scheme, and since the induced morphism h : \mathop{\mathrm{Spec}}(W) \to X' \times _ X X_ i maps the generic point of \mathop{\mathrm{Spec}}(W) into U \times _ X X_ i, we conclude that h factors through the closed subscheme X'_ i \subset X' \times _ X X_ i. We conclude that \{ f'_ i : X'_ i \to X'\} is a V covering. In particular, \coprod f'_ i is surjective. In particular \{ X'_ i \to X'\} is an fppf covering. Since an fppf covering is a ph covering (More on Morphisms, Lemma 37.48.7), we can find a standard ph covering \{ Y_ j \to X'\} refining \{ X'_ i \to X\} . Say this covering is given by a proper surjective morphism Y \to X' and a finite affine open covering Y = \bigcup Y_ j. Then the composition Y \to X is proper surjective and we conclude that \{ Y_ j \to X\} is a standard ph covering. This finishes the proof.
\square
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