To restart figure and table numbers in Appendix with correct link

In the LaTex/Lyx header, add the following package:

\usepackage{chngcntr}

Where the Appendix start, add the following script:

\appendix
\counterwithin{figure}{section} 
\counterwithin{table}{section}
\renewcommand{\thefigure}{A.\arabic{figure}}
\renewcommand{\thetable}{A.\arabic{table}}
% If figure/table numbers follow thos of the previous section, add: 
%\setcounter{figure}{0}
%\setcounter{table}{0}