you can create a node at each end of the lines and then connect these nodes. by adjusting the minimum size of node you can improve aesthetics.
(sorry for my google english)
\documentclass{article}
\usepackage{tikz}
\usetikzlibrary{arrows,decorations.pathmorphing,backgrounds,positioning,fit,petri,calc,shadows}
\begin{document}
\begin{tikzpicture}[
parent/.style={%
rounded corners,
thick,
draw=red!75,
fill=red!20,
thick,
inner ysep=2pt,
inner xsep=2pt,
minimum width = 4cm,
minimum height = 1.5cm,
align=center
},
child/.style={%
rounded corners,
thick,
draw=blue!90,
fill=blue!35,
thick,
inner ysep=2pt,
inner xsep=2pt,
minimum width = 4cm,
minimum height = 1.5cm,
align=center
},
grandchild/.style={%
rounded corners,
thick,
draw=green!90,
fill=green!35,
thick,
inner ysep=2pt,
inner xsep=2pt,
minimum width = 4cm,
minimum height = 1.5cm,
align=center
},
line/.style={%
semithick,
->,
shorten >=1pt,
>=stealth'
},
call/.style={%
blue,
semithick,
->,
shorten >=1pt,
>=stealth'
},
return/.style={%
red,
semithick,
->,
shorten >=1pt,
>=stealth'
}]
\node[child] (child) {Child};
\node[parent] at (-6,3) (parent 1) {Node 1\\I have manually\\connected this one};
\node[parent] at (0,3) (parent 2) {Node 2\\I have manually\\connected this one};
\node[parent] at (6,3) (parent 3) {Node 3\\I have manually\\connected this one};
\node[parent] at (-6,-3) (grandchild 1) {Node 4\\I have manually\\connected this one};
\node[parent] at (0,-3) (grandchild 2) {Node 5\\I have NOT manually\\connacted this one};
\node[parent] at (6,-3) (grandchild 3) {Node 6\\I have NOT manually\\connacted this one};
%draw three lines from each parent to each child
\draw [line] (parent 1.south east)node[above left](p1){} -- (child.north west)node[below right](c1){};
\draw [line] (parent 2.south)node[above](p2){} -- (child.north)node[below](c2){};
\draw [line] (parent 3.south west)node[above right](p3){} -- (child.north east) node[below left](c3){};
%draw three lines from each parent to each child
\draw [line] (grandchild 1.north east)node[below left,minimum size=2em](p4){} -- (child.south west)node[above right,minimum size=2em](c4){};
\draw [line] (grandchild 2.north)node[below,minimum size=2em](p5){} -- (child.south)node[above,minimum size=2em](c5){};
\draw [line] (grandchild 3.north west)node[below right](p6){} -- (child.south east)node[above left](c6){};
\foreach \nn in{1,2,3,4,5,6}{
\draw [call] (p\nn) to [bend right=15] (c\nn);
\draw [return] (c\nn) to [bend right=15] (p\nn);
}
\end{tikzpicture}
\end{document}!

I don't really get the question so I hope this is what you wanted. If you include a full document (such that we copy paste and see the problem on our systems) things are much more easier.
Here, you can change the default setting within a scope but your block
style had a node distance
which was resetting every time it is issued. I've made it 2mm such that we can see the difference easier.
\documentclass[tikz]{standalone}
\usetikzlibrary{arrows,shapes.geometric,positioning}
\begin{document}
\begin{tikzpicture}[decision/.style={diamond, draw, text width=4.5em, text badly centered, node distance=3.5cm, inner sep=0pt},
block/.style ={rectangle, draw, text width=6em, text centered, rounded corners, minimum height=4em, minimum height=2em},
cloud/.style ={draw, ellipse, minimum height=2em},
line/.style ={draw,-latex'},
node distance = 1cm,
auto]
\node [block] (1st) {1st};
\node [block, right= of 1st] (2nd1) {2nd1};
\begin{scope}[node distance=2mm and 10mm]%Here we change it for everything inside this scope
\node [block, above= of 2nd1] (2nd2) {2nd2};
\node [block, below= of 2nd1] (2nd3) {2nd3};
\node [block, right= of 2nd1] (3rd1) {3rd1};
\node [block, above= of 3rd1] (3rd2) {3rd2};
\node [block, above= of 3rd2] (3rd3) {3rd3};
\end{scope}
\node [block, below= of 3rd1] (3rd4) {3rd4};
\node [block, below= of 3rd4] (3rd5) {3rd5};
\path [line] (1st) -- (2nd1);
\path [line] (2nd1) -- (2nd2);
\path [line] (2nd1) -- (2nd3);
\path [line] (2nd2) -- (3rd3);
\path [line] (2nd1) -- (3rd1);
\path [line] (1st) -- (2nd1);
\end{tikzpicture}
\end{document}

Best Answer
That anchor indeed doesn't exist however you can cheat a little by taking the intersection of the east and south but if your linewidth is not negligible this needs a little bit more push using
[xshift=-\pgflinewidth]
.