Flextable label not created in rmarkdown

You need to use a format from bookdown to get cross references, see https://bookdown.org/yihui/rmarkdown-cookbook/cross-ref.html

---
title: "document title"
author: "author here"
date: "2022-01-20"
output: 
  bookdown::pdf_document2: 
    fig_caption: yes
    number_sections: yes
    toc: yes
    toc_depth: 4
    latex_engine: xelatex
    keep_tex: true
---

```{r, include = FALSE}
library(flextable)
library(knitr)
library(bookdown)

opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE, out.width = "85%", fig.align = "center")
```

```{r, tab.id = "anyTable", tab.cap = "Invented data"}
a = data.frame(id = LETTERS[1:3], x = 1:3)
flextable(a) |> theme_vanilla()
```

```{r secondTable}
b = data.frame(id = LETTERS[4:6], x = 4:6)
flextable(b) |> theme_vanilla() |> set_caption(caption = "This is secondTable")
```


# Bookdown crossreference

Trying anyTable: \@ref(tab:anyTable).

Trying secondTable: \@ref(tab:secondTable).