Problem using latexdiff and pdflatex with custom command

(OPs answer, moved from the question.)

I thought it would be more complex, but I found a solution. Using --exclude-textcmd allows the ignoring of tags. It works now.

--exclude-textcmd="section,subsection"

It's difficult without an MWE, but I would assume that the difficulty is with hyperref, which tries to include underlined/crossed out text as hyperlink given that it is part of a chapter.

The solution is to use texorpdfstring, which tells hyperref to use plain text for the hyperlinks. I can't remember the exact commands that latexdiff definds, but try something like that:

% Redefine these commands for chapter/sections and change below
\DeclareRobustCommand{\hsout}[1]{\texorpdfstring{\sout{#1}}{#1}}
\DeclareRobustCommand{\hwave}[1]{\texorpdfstring{\uwave{#1}}{#1}}

%DIF PREAMBLE EXTENSION ADDED BY LATEXDIFF
%DIF UNDERLINE PREAMBLE %DIF PREAMBLE
\RequirePackage[normalem]{ulem}% DIF PREAMBLE
\RequirePackage{color}\definecolor{RED}{rgb}{1,0,0}\definecolor{BLUE}{rgb}{0,0,1}%DIF PREAMBLE
\providecommand{\DIFadd}[1]{{\protect\textcolor{blue}{\hwave{#1}}}}% DIF PREAMBLE
\providecommand{\DIFdel}[1]{{\protect\textcolor{red}{\hsout{#1}}}}% DIF PREAMBLE
...

I had a problem with

\section{\DIFdelbegin \DIFdel{Conclusion}\DIFdelend \DIFaddbegin \DIFadd{Conclusions}\DIFaddend }

and Jörg's solution did not work for me. What worked was a manual substitution:

\section{\texorpdfstring{\DIFdelbegin \DIFdel{Conclusion}\DIFdelend \DIFaddbegin \DIFadd{Conclusions}\DIFaddend }{Conclusions}}