Okay, so it seems like nothing inside the config object is updated. I tried a few different solutions but in the end I simply needed to rerender the component to which the onDelete is passed with every reference update, like this:

<Entry
    v-for="(entry, index) in entries"
    :key="`${index}-${entry.entryActionConfig?.reference}`"
    :entry
></Entry>

-${entry.entryActionConfig?.reference} is the important part in here.