phd thesis, .eps .pdf graphics, missing embedded fonts, me turning nuts!

Question

i joined this forum because of a specific question, that i have already spent a few hours on investigating. i am very sure that you can help me, so that i can narrow down my problem.

i have turned in my phd thesis as a pdf to my universities's online publishing platform a few days ago. its a biochemical work lots of graphics, either .eps or .pdf. they came back to me saying that not all of the fonts were embedded into the pdf. i am not a lo9ng time tex'er through and through, but i thought that i know what i am doing, at least until now. i am confident to say that at least i am it affine.

my preamble looks like this:

\documentclass
[
%--Sprache
ngerman,
%--Seitenlayout
DIV=11,
BCOR=10mm,
a4paper,
headinclude=true,
footinclude=false,
twoside=true,
%--Schrift/Absätze
parskip=half,
fontsize=11pt,
headings=normal,
numbers=noenddot,
%--Entwurfsschalter
draft=false
]
                                    {scrreprt}
\usepackage                         {selnolig}
\usepackage[crop=off]               {auto-pst-pdf-lua}
\ifpdf
\usepackage                         {fontspec}
\usepackage                         {libertinus-otf}
\else
\usepackage[T1]                     {fontenc}
\usepackage[utf8]                   {inputenc}
\usepackage                         {erewhon}
\fi
%--Sprache
\usepackage[ngerman]                {babel}
\usepackage                         {lipsum}
%--Layout
\usepackage                         {tocloft}           % TOC/LOF/LOT
\usepackage[headsepline=0.5pt]      {scrlayer-scrpage}  % Layout
\usepackage                         {soul}
\setul{1pt}{.4pt}% 1pt below contents
\usepackage
    [
    final,
%   activate={true,nocompatibility},
%   tracking=true,
%   kerning=true,
%   spacing=true,
%   factor=1100,
%   stretch=10,
%   shrink=10
    ]                               {microtype}         % Textoptimierung
\usepackage
[
pdfauthor={Felix Maximilian Schilcher},
pdftitle={Barcoding von genomischer DNA und Anwendung im Bereich des DNA-Mappings},
colorlinks,
pdfpagelabels,
pdfstartview = FitH,
bookmarksopen = true,
bookmarksnumbered = true,
linkcolor = black,
plainpages = false,
hypertexnames = false,
citecolor = black
]                               {hyperref}

\usepackage[font={small}]           {caption}           % Unter-/Überschriften
\usepackage                         {siunitx}           % SI-Einheiten
\usepackage[version=4]              {mhchem}            % Chemie: Formeln
\usepackage                         {chemnum}           % Chemie: Nummerierungen
\usepackage                         {longtable}         % multi-page Tabellen
\usepackage                         {graphicx}          % Grafiken
\usepackage                         {float}
\usepackage                         {array}
\usepackage                         {calc}
\usepackage                         {lscape}
\usepackage                         {setspace}
%---------------------------------
%-----------Einstellungen---------
%---------------------------------
\captionsetup
{
    format=plain,
    labelfont={sf,bf,small},
    textfont={sf,small}
}
\sisetup
{
    locale = DE, 
    detect-all,
    group-separator = ,,
    range-phrase = --,
    separate-uncertainty,
    multi-part-units = single
}
\newcommand{\itJ}{{\addfontfeature{Alternate=0}\textit{J}}}
%\renewcommand*\pm{\raisebox{.2ex}{$\scriptstyle\pm$}}
\setchemnum{replace-style = \fontsize{8}{9.5}\sffamily}
\setcounter{tocdepth}{2}
\setcounter{secnumdepth}{3}
%-- Kopf- und Fußzeilen
\pagestyle{scrheadings}
%\chead{\headmark}
\automark{chapter}
%-- Überschriften
\renewcommand\chapterheadstartvskip{\vspace{-1cm}}
\renewcommand\chapterheadendvskip{\vspace{0.5cm}}
\RedeclareSectionCommand[tocindent=0.0cm,tocbeforeskip=0.02cm,beforeskip=0.3cm,afterskip=0.25cm]{section}
\RedeclareSectionCommand[tocindent=0.1cm,tocbeforeskip=0.01cm,beforeskip=0.2cm,afterskip=0.15cm]{subsection}
\RedeclareSectionCommand[tocindent=0.2cm,tocbeforeskip=0.00cm,beforeskip=0.1cm,afterskip=0.05cm]{subsubsection}
\setlength{\cftfigindent}{0pt} % remove indentation from figures in lof
\setlength{\cfttabindent}{0pt} % remove indentation from tables in lot
%-- Tabellenüberschriften/Bildunterschiften
\setlength{\captionmargin}      {1.0em} %links/rechts margin
\setlength{\abovecaptionskip}   {2ex} %abstand reset
\setlength{\belowcaptionskip}   {1ex} %abstand reset
\renewcommand{\cftdotsep}{1}
\newcommand{\etal}{\textsc{Et.,Al.~}}
%-- Hurenkinder und Schusterjungen verhindern
\clubpenalty10000
\widowpenalty10000
\displaywidowpenalty=10000

when i go thorugh the pdf settings - the font tab doesn't show all fonts as embedded subsets whatsoever. i followed this link "https://www.karlrupp.net/2016/01/embed-all-fonts-in-pdfs-latex-pdflatex/" - but modifying the ps2pdf command line in the texlive settings didnt do anything.

similar to a post "https://tex.stackexchange.com/questions/202709/how-to-embed-all-fonts-with-pdflatex-in-combination-with-pstricks-and-auto-pst-p" i have not 1 but 20 T3 fonts that are not embedded and other than that:

helvetica helvetica-bold helvetica-oblique

my pdf contains serveral eps and pdf file from powerpoint, mathlab, origin, chemdraw and so on. i am sure the fonts come from there. problem is, that last time i edited those files was more than 2 years ago and i dont even have the software (origin, chemdraw, ...) liceses anymore.

i am so frustrated, this is the very last challenge regarding my phd, can u please give me a hint at least what to search for next.

damn it, thank you :)

felix