For some unknown reason the following produces an error in classicthesis:
% at the beginning of classicthesis-config.tex
\renewcommand{\d}{\mathbf{d}}
\begin{document}
$\d$
\end{document}
The error says \d is invalid in math mode and $ is missing. It doesn't occur with a simple test case, for sure it's related to the template settings.
Best Answer
You could just put the redefinition in the document so after classicthesis and/or hyperref have defined it, but if you don't want to do that
Probably works (although untested as no example supplied).