documentclass[11pt]{article}
pagestyle{empty}
usepackage{graphicx}
usepackage{blindtext}
usepackage[colorlinks=true,
,citecolor=blue
,linkcolor=blue]{hyperref}

begin{document}
section{Section 1}
label{section1}
blindtext

begin{figure}[t]
    centering
    includegraphics[width=.49columnwidth]{example-image-a}
    caption{Dummy caption cite{1} (see figure~ref{fig3} in
      section~ref{section3}).label{fig1}}
end{figure}

section{Section 2}
label{section2}
blindtext

begin{figure}[t]
    centering
    includegraphics[width=.49columnwidth]{example-image-b}
    caption{Dummy caption cite{2} (see figure~ref{fig1} in
      section~ref{section1}).label{fig2}}
end{figure}

section{Section 3}
label{section3}
blindtext
blindtext

begin{figure}[t]
    centering
    includegraphics[width=.49columnwidth]{example-image-c}
    caption{Dummy caption cite{3} (see figure~ref{fig2}
      section~ref{section2}).label{fig3}}
end{figure}

begin{thebibliography}{9}

bibitem{1}
Dummy bibibtem

bibitem{2}
Dummy bibibtem

bibitem{3}
Dummy bibibtem

end{thebibliography}
end{document}

latexmk -pdf mydoc.tex; cp mydoc.aux mydoc-bk.aux

pdflatex "AtBeginDocument{usepackage[figuresonly,nolists]{endfloat}} input{Float.tex}"

begin{figure}[t]
  centering
  includegraphics[width=.49columnwidth]{example-image-a}
  caption{Dummy caption cite{1} (see figure~ref{fig3} in
    section~ref{section3}).label{fig1}}
end{figure}
efloatseparator

begin{figure}[t]
  centering
  includegraphics[width=.49columnwidth]{example-image-b}
  caption{Dummy caption cite{2} (see figure~ref{fig1} in
    section~ref{section1}).label{fig2}}
end{figure}
efloatseparator

begin{figure}[t]
  centering
  includegraphics[width=.49columnwidth]{example-image-c}
  caption{Dummy caption cite{3} (see figure~ref{fig2}
    section~ref{section2}).label{fig3}}
end{figure}
efloatseparator

documentclass[11pt]{article}
pagestyle{empty}
usepackage{graphicx}
usepackage{blindtext}
usepackage[colorlinks=true,
,citecolor=blue
,linkcolor=blue]{hyperref}

defefloatseparator{clearpage}

begin{document}

input{Float.fff}

end{document}

pdflatex myNewDoc.tex

pdflatex -jobname=mydoc "nofilesRequirePackage{xcomment} xcomment{figure}nofilesAtBeginDocument{letoldendfigureendfigure defendfigure{oldendfigureclearpage}} input{mydoc.tex}"