You adjusted
\theenumi, \theenumii, \theenumiii
and
\labelenumi, \labelenumii, \labelenumiii.
I think you need to also adjust
\p@enumi, \p@enumii, \p@enumiii.
These macros deliver prefix/postfix to \the⟨counter⟩ when \refstepcounter stores cross-referencing-data used by \label as macro \@currentlabel.
I don't know what \myem, \myex and \@listinterlined are, but I assume they are some units/lengths and I defined them on my own, with weird values. ;-)
Does the example deliver the output you desire?
\errorcontextlines=10000
\documentclass{article}
%\usepackage{hyperref}
\makeatletter
\def\myem{em}
\def\myex{ex}
\def@listinterlined{.5\baselineskip}
\newenvironment{functionalProcesosAutomaticos}
{%%%%
\bgroup
\renewcommand\baselinestretch{1.3}%%%%%%%%%%%%
\typeout{Begining enumeration}%%%%%%%%%%%%
\advance@enumdepth @ne
\ifnum
@enumdepth >4 @toodeep
\else
\def@enumctr{enum\romannumeral\the@enumdepth}%%%%
\list{\csname label@enumctr\endcsname}%%%%
{%%%%
\small
\partopsep=0\myem\relax
\topsep=@listinterlined\relax
\itemsep=@listinterlined\relax
\parsep=@listinterlined\relax
\advance\topsep by .3\myem\relax
\advance\itemsep by .15\myem\relax
\itemindent=0\myem\relax
\rightmargin=5\myex\relax
\leftmargin=8\myex\relax
\labelsep=1\myex\relax
\labelwidth=3\myex\relax
\usecounter{@enumctr}%
\renewcommand{\theenumi}{SGPA\arabic{enumi}}%%%%
\renewcommand{\theenumii}{\theenumi.\arabic{enumii}}%%%%
\renewcommand{\theenumiii}{\theenumii.\arabic{enumiii}}%%%%
\renewcommand{\theenumiv}{\theenumiii.\arabic{enumiv}}%%%%
\renewcommand{\p@enumi}{}%%%%
\renewcommand{\p@enumii}{}%%%%
\renewcommand{\p@enumiii}{}%%%%
\renewcommand{\p@enumiv}{}%%%%
% \renewcommand{\p@enumii}[1]{##1.--}%%%%
% \renewcommand{\p@enumiii}[1]{##1.--}%%%%
% \renewcommand{\p@enumiv}[1]{##1.--}%%%%
\renewcommand{\labelenumi}{\textbf{\theenumi}}%%%%
\renewcommand{\labelenumii}{\textbf{\theenumii}}%%%%
\renewcommand{\labelenumiii}{\textbf{\theenumiii}}%%%%
\renewcommand{\labelenumiv}{\textbf{\theenumiv}}%%%%
% \renewcommand{\labelenumii}{\textbf{\theenumii.--}}%%%%
% \renewcommand{\labelenumiii}{\textbf{\theenumiii.--}}%%%%
% \renewcommand{\labelenumiv}{\textbf{\theenumiv.--}}%%%%
}%%%%
\fi
}{%%%%
\ifnum
@enumdepth >4
\else
\expandafter\endlist
\fi
\typeout{Ending enumeration}%%%%
\egroup
}
\makeatother
\begin{document}
\ref{AnotherItem}
\ref{AnotherNestedItem}
\ref{AnotherNestedNestedItem}
\ref{AnotherNestedNestedNestedItem}
\begin{functionalProcesosAutomaticos}
\item An item
\item\label{AnotherItem} Another item
\item Yet another item
\begin{functionalProcesosAutomaticos}
\item A nested item
\item\label{AnotherNestedItem} Another nested item
\item Yet another nested item
\begin{functionalProcesosAutomaticos}
\item A nested nested item
\item\label{AnotherNestedNestedItem} Another nested nested item
\item Yet another nested nested item
\begin{functionalProcesosAutomaticos}
\item A nested nested nested item
\item\label{AnotherNestedNestedNestedItem} Another nested nested nested item
\item Yet another nested nested nested item
%\begin{functionalProcesosAutomaticos}
%\item A nested nested nested nested item
%\item\label{AnotherNestedNestedNestedNestedItem} Another nested nested nested nested item
%\item Yet another nested nested nested nested item
%\end{functionalProcesosAutomaticos}
\end{functionalProcesosAutomaticos}
\end{functionalProcesosAutomaticos}
\end{functionalProcesosAutomaticos}
\end{functionalProcesosAutomaticos}
\end{document}

\listinterlined{0.1\myem}``` is the list interlined, and yes, it is what I'm looking for but it doesn't work in my template :/ It doesn't compile the document, so I think at this point is a template issue, thank you anyway– Sugar G. García Jul 13 '21 at 17:56