Proof.
Part (1) follows from a combination of Lemmas 103.6.1 and 103.7.2. The proof of (2) is analogous to the proof of Lemma 103.6.3. Let $\mathcal{F}$ of a sheaf of $\mathcal{O}_\mathcal {X}$-modules on $\mathcal{X}_{fppf}$.
First, suppose there is a morphism $a : \mathcal{U} \to \mathcal{X}$ which is surjective, flat, locally of finite presentation, quasi-compact, and quasi-separated such that $a^*\mathcal{F}$ is locally quasi-coherent and has the flat base change property. Then there is an exact sequence
\[ 0 \to \mathcal{F} \to a_*a^*\mathcal{F} \to b_*b^*\mathcal{F} \]
where $b$ is the morphism $b : \mathcal{U} \times _\mathcal {X} \mathcal{U} \to \mathcal{X}$, see Sheaves on Stacks, Proposition 96.19.7 and Lemma 96.19.10. Moreover, the pullback $b^*\mathcal{F}$ is the pullback of $a^*\mathcal{F}$ via one of the projection morphisms, hence is locally quasi-coherent and has the flat base change property, see Proposition 103.8.1. The modules $a_*a^*\mathcal{F}$ and $b_*b^*\mathcal{F}$ are locally quasi-coherent and have the flat base change property by Proposition 103.8.1. We conclude that $\mathcal{F}$ is locally quasi-coherent and has the flat base change property by Proposition 103.8.1.
Choose a scheme $U$ and a surjective smooth morphism $x : U \to \mathcal{X}$. By part (1) it suffices to show that $x^*\mathcal{F}$ is locally quasi-coherent and has the flat base change property. Again by part (1) it suffices to do this (Zariski) locally on $U$, hence we may assume that $U$ is affine. By Morphisms of Stacks, Lemma 101.27.14 there exists an fppf covering $\{ a_ i : U_ i \to U\} $ such that each $x \circ a_ i$ factors through some $f_ j$. Hence the module $a_ i^*\mathcal{F}$ on $(\mathit{Sch}/U_ i)_{fppf}$ is locally quasi-coherent and has the flat base change property. After refining the covering we may assume $\{ U_ i \to U\} _{i = 1, \ldots , n}$ is a standard fppf covering. Then $x^*\mathcal{F}$ is an fppf module on $(\mathit{Sch}/U)_{fppf}$ whose pullback by the morphism $a : U_1 \amalg \ldots \amalg U_ n \to U$ is locally quasi-coherent and has the flat base change property. Hence by the previous paragraph we see that $x^*\mathcal{F}$ is locally quasi-coherent and has the flat base change property as desired.
$\square$
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