ifdefinedHCode
% HTML branch...
else
% PDF branch...
fi

ifdefinedHCode
    documentclass{book}
else
    documentclass[11pt,a4paper]{book}
    usepackage{longtable}
    usepackage{tabu}
fi

begin{document}

% Define table header differently if we are produced HTML or PDF
ifdefinedHCode
  %for HTML
  begin{tabular}{|l|l|}
  hline
  A & B \
  hline
else
  % For PDF
  begin{longtabu} to linewidth {|X|X|}
  hline
  rowfont A & B \ hline
  hline
  endhead
fi

1 & 2 \ hline
3 & 4 \ hline

% Close correctly the table depending on output
ifdefinedHCode
  % for HTML
  end{tabular}
else
  % For PDF
  end{longtabu}
fi

end{document}

Runaway argument?
global advance c@LT@chunks @ne global LT@rows z@ setbox z@ vbox ETC.

! Forbidden control sequence found while scanning use of LT@nofcols.
<inserted text>
par
l.35      end{tabular}

?