The problem here is that you are trying to round a corner in a path with two points that are very close to each other:
- The end point of the second
arc
- The
cycle
point that close your path.
When I compile your code, I abtain an awful glitch:
I suggest here an alternative the solution based on cutting one of the arcs by the middle with an auxiliary path that find the middle point:
\documentclass{article}
\usepackage{tikz}
\begin{document}
\usetikzlibrary{ext.topaths.arcthrough}
\begin{tikzpicture}[x=1cm,y=1cm]
\draw [help lines] (0,0) grid (4,6);
\draw[rounded corners, fill=cyan!20]
(4,2) arc [start angle=45, end angle=135, radius=2.828]
arc [start angle=-131.81, end angle=-48.19, radius=3] -- cycle ;
\begin{scope}[yshift=2cm]
% Auxiliar path to calculate coordinate (A)
\path
(4,2)
arc [start angle=45, end angle=135, radius=2.828]
node[pos=0.5, circle, fill=red, inner sep=1pt] (A) {}
;
\draw[rounded corners, fill=cyan!20]
(A)
arc [start angle=90, end angle=135, radius=2.828]
arc [start angle=-131.81, end angle=-48.19, radius=3]
arc [start angle=45, end angle=90, radius=2.828]
;
\end{scope}
\end{tikzpicture}
\end{document}