% arara: pdflatex
% arara: makeglossaries
% arara: pdflatex
\documentclass{article}

\usepackage{etoolbox}
\usepackage
 [
  indexcrossrefs=false% cross-ref indexing performed explicitly
 ]
 {glossaries-extra}

\makeglossaries

% Keep a list of entries that have been indexed
\newcommand*{\indexedlist}{}
\renewcommand*{\glsxtrdowrglossaryhook}[1]{%
  \xifinlist{#1}{\indexedlist}{}{\listxadd{\indexedlist}{#1}}%
}

\newglossaryentry{sample1}{name={sample 1},description={an example}}
\newglossaryentry{sample2}{name={sample 2},description={an
example},see={sample1}}
\newglossaryentry{sample3}{name={sample 3},description={an
example},see={sample2}}

\newglossaryentry{sample4}{name={sample 4},description={an example}}

\begin{document}
This is sample document.

\gls{sample3}.

\printglossaries

% index all the cross-referenced entries that haven't been used:
\glsxtraddallcrossrefs

Entries that haven't been indexed:
\forglsentries{\thislabel}{\xifinlist{\thislabel}{\indexedlist}{}{\space\thislabel}}.

\end{document}