After doing some research, I realized that there are parts of the .sty file that govern how the "list of Algorithms" are organized. This file creates a file with extension .lom that keeps all information about the algorithm list. In this file, the labels of appendix algorithms are linked to algorithms in the body! Please find below parts of the .sty file that talk about "list of Algorithms" rules. I am wondering if someone can help me with debugging these lines.
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\def\listofalgorithms{%
\newpage
\addcontentsline{toc}{chapter}{LIST OF ALGORITHMS}
\@restonecolfalse\if@twocolumn\@restonecoltrue\onecolumn\fi
\hbox{ }
\twoinmar
\centerline{\large\bf LIST OF ALGORITHMS}
\vspace{0.7in}
\begin{doublespace}
\@starttoc{lom}\if@restonecol\twocolumn\fi
\addtocontents{lom}{\noindent\underline{\bf Algorithm}\hfill\rm\protect\newline}
\end{doublespace}
\pagestyle {empty}
}
\newcounter{algorithm}[chapter]
\def\thealgorithm{\@arabic\c@chapter.\@arabic\c@algorithm}
\def\fps@algorithm{tbp}
\def\ftype@algorithm{1}
\def\ext@algorithm{lom}
\def\fnum@algorithm{Algorithm\thealgorithm}
\def\algorithm{\@float{algorithm}}
\let\endalgorithm\end@float
\@namedef{algorithm*}{\@dblfloat{algorithm}}
\@namedef{endalgorithm*}{\end@dblfloat}