Link to supplementary table links to main text table in R Markdown - r

Question

I have been using the following LaTeX command to create supplementary tables in my R Markdown documents:
\newcommand{\beginsupplement}{\setcounter{table}{0} \renewcommand{\thetable}{S\arabic{table}} \setcounter{figure}{0} \renewcommand{\thefigure}{S\arabic{figure}}}
However, recently the linkage has broken. For example, when clicking on "Table S1" in-text, I will be taken to Table 1. Please see the example below:
---
title: 'Test Rmd document'
output:
pdf_document
header-includes:
- \newcommand{\beginsupplement}{\setcounter{table}{0} \renewcommand{\thetable}{S\arabic{table}} \setcounter{figure}{0} \renewcommand{\thefigure}{S\arabic{figure}}}
---
```{r, setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(kableExtra)
library(tibble)
```
## Main body
This is a main text table (\autoref{main_table}). There is also a supplementary table (\autoref{supplementary_table}).
```{r}
table <- tibble(a = 1:3, b = 4:6)
kable(table,
caption = "Main body table \\label{main_table}",
format = "markdown")
```
\newpage
# Supplementary materials
\beginsupplement
```{r}
table <- tibble(a = 7:9, b = 10:12)
kable(table,
caption = "Supplementary table \\label{supplementary_table}",
format = "markdown")
```
Rendering the above gives this pdf document. Why is "(Table S1)" linking to Table 1?