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It turns out the issue wasn’t with Shopify at all, but rather the v-bind:key attribute missing on v-for in order to work with a transition group.
<div v-for="product in filteredProducts" v-if="product.available" v-bind:key="product">
Prior to that everything nested in the transition-group was being removed, and would only work for the first item.
Source:stackexchange.com