Font too thin and lines disappearing

Question

I am having issues getting a nice font for my paper as whatever I try, the serif font just looks way too thin in places and parts of characters are disappearing.

You can see it in the "A", "e", "g" "s", "o" and some other places.

My preamble looks like this:

\documentclass[12pt]{report}

\usepackage[tmargin=2cm,rmargin=1in,lmargin=1in,margin=0.85in,bmargin=2cm,footskip=.2in]{geometry}
\usepackage{amsmath,amsfonts,amsthm,amssymb,mathtools}
\usepackage{mathtools}
\usepackage{hyperref,theoremref}
\hypersetup{
    pdftitle={Thesis},
    colorlinks=true, linkcolor=doc!90,
    bookmarksnumbered=true,
    bookmarksopen=true
}
\usepackage{multicol,array}
\usepackage{tikz-cd}
\usepackage[ruled,vlined,linesnumbered]{algorithm2e}
\usepackage{comment}
\usepackage{import}
\usepackage{microtype}
\usepackage{fancyhdr}
\usepackage{tikzsymbols}
\usepackage{tabularray}


\usepackage{tkz-graph}

\usepackage{xcolor}
\usepackage{libertine}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{helvet}

\DisableLigatures{encoding = *, family = *}
\begin{document}


This chapter will describe a language modelling framework that seeks to solve the previously described problems. The framework automatically induces a hierarchical, graph based N-Gram structure from raw text, which is easy to explain, predict and efficiently updateable. The structure models the text as a hyperedge which has been compressed into a grammar-like structure of nested hyperedges. The structure avoids repetitions and other redundancy while maintaining all of the containment relations between elements which are used for a count-based language modelling.


\end{document}

I compile in vs-code using Latex Workshop using the lualatex command:

    "latex-workshop.latex.tools": [
    
        {
            "name": "latexmk",
            "command": "lualatex",
            "args": [
                "-synctex=1",
                "-interaction=nonstopmode",
                "-file-line-error",
                "--output-directory=%OUTDIR%",
                "%DOC%"
            ],
            "env": {}
        },
    ],

Answer 1

The posted code produces

Your image does not appear to be using Linux Libertine, which can not happen unless you got an error or warning about missing files. (After any error the pdf is not intended to be usable, just a debugging aid)

what is the ouput of pdffonts on your pdf, it should be:

name                                 type              encoding         emb sub uni object ID
------------------------------------ ----------------- ---------------- --- --- --- ---------
KYKDBY+LinLibertineT                 Type 1            Custom           yes yes yes     11  0

The document is set up for 8 bit fonts: if you use lualatex you get the warning

LaTeX Font Warning: Font shape `T1/LinLibertine(0)/m/n' undefined
(Font)              using `T1/cmr/m/n' instead on input line 112.

so uses cm fonts not linux libertine. It looks as if you only have bitmap T1 fonts installed (which means most likely you are usiung miktex and have not installed the cm-super package with type1 cm fonts)