How to knitr beamer slides using Frankfurt theme without loosing navigation circles

After updating R and packages my beamer slides using Frankfurt theme no longer include the navigation circles at the top.

A mock Rmd file to demonstrate:

---
title: "Untitled"
output: 
  beamer_presentation:
    theme: "Frankfurt"
    # keep_tex: true
    slide_level: 3
header-includes: 
- \AtBeginSubsection{}
- \AtBeginSection{}
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```

# Intro

## .

### R Markdown

This is an R Markdown presentation. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document.

# Example

## .

### Slide with Bullets

- Bullet 1
- Bullet 2
- Bullet 3

### Slide with R Output

```{r cars, echo = TRUE}
summary(cars)
```

### Slide with Plot

```{r pressure}
plot(pressure)
```

Which gives ...

enter image description here

I can get the navigation circles to appear by setting keep_tex: true in the YAML and compiling the .tex file ...

enter image description here

... but this seems like an extra unnecessary step that was not previously required?

R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] sessioninfo_1.1.1

loaded via a namespace (and not attached):
 [1] compiler_3.6.1   assertthat_0.2.1 cli_1.1.0        htmltools_0.3.6  tools_3.6.1      withr_2.1.2     
 [7] rstudioapi_0.10  yaml_2.2.0       crayon_1.3.4     Rcpp_1.0.2       rmarkdown_1.15   knitr_1.25      
[13] xfun_0.9         digest_0.6.20    packrat_0.5.0    evaluate_0.14 



EDIT: As requested, the .tex file generated when setting keep_tex: true in the YAML

\PassOptionsToPackage{unicode=true}{hyperref} % options for packages loaded elsewhere
\PassOptionsToPackage{hyphens}{url}
%
\documentclass[
  ignorenonframetext,
]{beamer}
\usepackage{pgfpages}
\setbeamertemplate{caption}[numbered]
\setbeamertemplate{caption label separator}{: }
\setbeamercolor{caption name}{fg=normal text.fg}
\beamertemplatenavigationsymbolsempty
% Prevent slide breaks in the middle of a paragraph:
\widowpenalties 1 10000
\raggedbottom
\setbeamertemplate{part page}{
  \centering
  \begin{beamercolorbox}[sep=16pt,center]{part title}
    \usebeamerfont{part title}\insertpart\par
  \end{beamercolorbox}
}
\setbeamertemplate{section page}{
  \centering
  \begin{beamercolorbox}[sep=12pt,center]{part title}
    \usebeamerfont{section title}\insertsection\par
  \end{beamercolorbox}
}
\setbeamertemplate{subsection page}{
  \centering
  \begin{beamercolorbox}[sep=8pt,center]{part title}
    \usebeamerfont{subsection title}\insertsubsection\par
  \end{beamercolorbox}
}
\AtBeginPart{
  \frame{\partpage}
}
\AtBeginSection{
  \ifbibliography
  \else
    \frame{\sectionpage}
  \fi
}
\AtBeginSubsection{
  \frame{\subsectionpage}
}
\usepackage{lmodern}
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[T1]{fontenc}
  \usepackage[utf8]{inputenc}
  \usepackage{textcomp} % provides euro and other symbols
\else % if luatex or xelatex
  \usepackage{unicode-math}
  \defaultfontfeatures{Scale=MatchLowercase}
  \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
\fi
\usetheme[]{Frankfurt}
% use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\IfFileExists{microtype.sty}{% use microtype if available
  \usepackage[]{microtype}
  \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
\makeatletter
\@ifundefined{KOMAClassName}{% if non-KOMA class
  \IfFileExists{parskip.sty}{%
    \usepackage{parskip}
  }{% else
    \setlength{\parindent}{0pt}
    \setlength{\parskip}{6pt plus 2pt minus 1pt}}
}{% if KOMA class
  \KOMAoptions{parskip=half}}
\makeatother
\usepackage{xcolor}
\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
\hypersetup{
  pdftitle={Untitled},
  pdfborder={0 0 0},
  breaklinks=true}
\urlstyle{same}  % don't use monospace font for urls
\newif\ifbibliography
\usepackage{color}
\usepackage{fancyvrb}
\newcommand{\VerbBar}{|}
\newcommand{\VERB}{\Verb[commandchars=\\\{\}]}
\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}
% Add ',fontsize=\small' for more characters per line
\usepackage{framed}
\definecolor{shadecolor}{RGB}{248,248,248}
\newenvironment{Shaded}{\begin{snugshade}}{\end{snugshade}}
\newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{#1}}
\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.77,0.63,0.00}{#1}}
\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
\newcommand{\BuiltInTok}[1]{#1}
\newcommand{\CharTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{#1}}
\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.64,0.00,0.00}{\textbf{#1}}}
\newcommand{\ExtensionTok}[1]{#1}
\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\ImportTok}[1]{#1}
\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
\newcommand{\NormalTok}[1]{#1}
\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}}
\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}}
\newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
\newcommand{\RegionMarkerTok}[1]{#1}
\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\StringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\usepackage{graphicx,grffile}
\makeatletter
\def\maxwidth{\ifdim\[email protected]@width>\linewidth\linewidth\else\[email protected]@width\fi}
\def\maxheight{\ifdim\[email protected]@height>\textheight\textheight\else\[email protected]@height\fi}
\makeatother
% Scale images if necessary, so that they will not overflow the page
% margins by default, and it is still possible to overwrite the defaults
% using explicit options in \includegraphics[width, height, ...]{}
\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
\setlength{\emergencystretch}{3em}  % prevent overfull lines
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
\setcounter{secnumdepth}{-2}

% set default figure placement to htbp
\makeatletter
\def\[email protected]{htbp}
\makeatother

\AtBeginSubsection{}
\AtBeginSection{}

\title{Untitled}
\date{}

\begin{document}
\frame{\titlepage}

\hypertarget{intro}{%
\section{Intro}\label{intro}}

\hypertarget{section}{%
\subsection{.}\label{section}}

\begin{frame}{R Markdown}
\protect\hypertarget{r-markdown}{}

This is an R Markdown presentation. Markdown is a simple formatting
syntax for authoring HTML, PDF, and MS Word documents. For more details
on using R Markdown see \url{http://rmarkdown.rstudio.com}.

When you click the \textbf{Knit} button a document will be generated
that includes both content as well as the output of any embedded R code
chunks within the document.

\end{frame}

\hypertarget{example}{%
\section{Example}\label{example}}

\hypertarget{section-1}{%
\subsection{.}\label{section-1}}

\begin{frame}{Slide with Bullets}
\protect\hypertarget{slide-with-bullets}{}

\begin{itemize}
\tightlist
\item
  Bullet 1
\item
  Bullet 2
\item
  Bullet 3
\end{itemize}

\end{frame}

\begin{frame}[fragile]{Slide with R Output}
\protect\hypertarget{slide-with-r-output}{}

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{summary}\NormalTok{(cars)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00
\end{verbatim}

\end{frame}

\begin{frame}{Slide with Plot}
\protect\hypertarget{slide-with-plot}{}

\includegraphics{temp_files/figure-beamer/pressure-1.pdf}

\end{frame}

\end{document}