When making a reference to an equation or image, the subsequent text after the reference is in the same font style as the reference

Question

I have a strange problem, whenever I make a reference in the body of the text e.g. ....in Equation \ref{MyEquationOne} all subsequent main body text after the reference is changed to the same font style and formatting configuration as the equation or figure reference -- And I can't see why:

Here is an example

    \documentclass{report}

    \usepackage[reqno]{amsmath}
    \usepackage{Baskervaldx}
    \usepackage[baskervaldx,upint]{newtxmath}
    \usepackage[margin=25mm]{geometry}
    \usepackage[margin=9mm]{caption}
    \usepackage[font={small}]{caption}
    \usepackage[hang,bottom]{footmisc}
    \usepackage{natbib}
    \usepackage{graphicx}
    \usepackage{subfiles}
    \usepackage{amsfonts}
    \usepackage{graphicx}\graphicspath{{figures/}}
    \usepackage{array}
    \usepackage{amsmath}
    \usepackage{amssymb}
    \usepackage{upgreek}
    \usepackage{subcaption}
    \usepackage{listings}
    \usepackage{color}
    \usepackage{float}
    \usepackage{dcolumn}
    \usepackage{fancyhdr}
    \usepackage{xfrac}
    \usepackage{pdfpages}
    \usepackage{epigraph}
    \usepackage{etoolbox}
    \usepackage{booktabs}
    \usepackage{titlesec}
    \usepackage{bm}
    \usepackage{tocloft}
    \usepackage{blindtext}
    \usepackage{circuitikz}
    \usepackage{tikz}\usetikzlibrary{arrows,decorations,shapes}\usetikzlibrary{decorations.markings,decorations.pathmorphing}

    \renewcommand{\contentsname}{\centering\scshape\LARGE\normalfont{TABLE OF CONTENTS}}
    \renewcommand{\listfigurename}{\centering\scshape\LARGE\normalfont{LIST OF FIGURES}}
    \renewcommand{\listtablename}{\centering\scshape\LARGE\normalfont{LIST OF TABLES}}
    \renewcommand{\bibname}{\centering\scshape\LARGE\normalfont{BIBLIOGRAPHY}}
    \renewcommand{\thechapter}{\scshape\Roman{chapter}}
        \titleformat{\chapter}{\centering\scshape\LARGE\normalfont\color{black}}{\thechapter.}{1pt}{}
        \makeatletter
        \def\@makechapterhead#1{%
            \vspace*{-5em}% Space above number
            {
                \parindent \z@  \scshape
                \interlinepenalty\@M
                \Large\centering \scshape{\thechapter}%
                \par\vspace{1mm}% Space between number and title
                \MakeUppercase{#1}%
                \par\vspace{2.5em}% Space between title and text
            }
        }
        \makeatother

    \makeatletter
    \patchcmd{\epigraph}{\@epitext{#1}}{\itshape\@epitext{#1}}{}{}
    \makeatother
    \setlength\epigraphwidth{16cm}
    \setlength\epigraphrule{0pt}

    \numberwithin{equation}{section}

    \begin{document}

    \chapter{THE PEAK LINESHAPE}

      \section*{Introduction}
Here I go making some point about something or other, then BAM! I need an equation which looks like,
\begin{equation}
      E = m c^{2} \text{.}
      \label{EQN:MyFirstEquation}
    \end{equation}
After blathering on some more I want to talk about Equation \ref{EQN:MyFirstEquation}, but Oh no! Now the main body text has been changed -- help!
\end{document}

Answer 1

Your "minimal working example" is not that minimal. Here is a version that removes lots of extraneous stuff and enables one to diagnose the problem:

\documentclass{report}
\usepackage{amsmath}
\renewcommand{\thechapter}{\scshape\Roman{chapter}}
\numberwithin{equation}{section}

\begin{document}
\chapter{THE PEAK LINESHAPE}
\section*{Introduction}
Here I go making some point about something or other, then BAM! I need an equation which looks like,
\begin{equation}
  E = m c^{2} \text{.}
  \label{EQN:MyFirstEquation}
\end{equation}
After blathering on some more I want to talk about Equation \ref{EQN:MyFirstEquation}, but Oh no! Now the main body text has been changed -- help!
\end{document}

The problem is with the redefinition of \thechapter. You have used \scshape, which then affects all the text that follows. A better method would be to use:

\renewcommand{\thechapter}{\textsc{\Roman{chapter}}}