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"\renewcommand\citet{\autocite}" is wrong because \citet takes one argument, thus \renewcommand{\citet}[1]{\autocite{#1}} . You should test without this first. Your document is a mess! Do you still have calls to \bibliography AND \addbibresource at the same time? Test your new biber on minimal ...

A lot is going on there, so you should try to reduce the problem somehow. Try with a .bib file with only one entry. Try \usepackage[...]{biblatex} instead of \usepackage[...]{biblatex-chicago}. Try removing all but necessary packages. In short, do all the work we'd have to do to debug your problem ...

You'll have to play with the commands like
\renewcommand{\cftsecfont}{\normalfont\small}
\setlength{\cftbeforechapskip}{0.1em}

for \cftchapfont, \cftsubsecfont, \cftbeforechapskip, \cftbeforesecskip

These are some sub-normal font sizes: \small, \footnotesize, \scriptsize .

\cftbefore...skip ...

Why don't you try your MWE with the .bib file from "two simple examples". Debugging is hard with so many entries. Biber+biblatex is probably broken (don't know why), so you might need to stick to bibtex8.
Btw. if your .bib file is in the same directory as your main document, biblatex in LyX 2.2 ...

Have you checked if the "two simple examples" from https://wiki.lyx.org/BibTeX/Biblatex work?
You're using some absolute paths, but what exactly do you have for [Home]?
I don't think this is the right way of redefining \renewcommand\citet{\autocite} as well.

Seems like one } is missing here.

One more thing I would suggest is putting the text-width settings (the \areaset stuff) also inside the preamble file, so it can be modified on a per-document basis.
I don't think this is ever going to happen, A.M. is very conservative on changing classicthesis.sty (for lots of reasons)
But what ...

Please provide more information. What's your operating system, what was the previous version, how did you install v2.0.0, are there any remains of the previous version in your install directory, have you tried uninstalling then installing again, what error messages do you get and at what stage ...

This problem only exists in MiKTeX as its package manager installs and then uses system-wide classicthesis-preamble.sty. We are currently working on fixing this by making the preamble file a .tex and not a .sty any more (MiKTeX cares only about installing .sty's)
For now, changing the name of the ...

You'll find the relevant code in classicthesis.sty, in the section "layout of the chapter-, section-, subsection-, subsubsection-, paragraph and description-headings" (below line 350).
I'm putting in bold the commands you'll probably want change or replace

\titleformat{\chapter}[display]%
{\relax ...