The icons path is currently hardcoded and it is created during configuration time at build stage. At the moment, the only way to change the icons for a Synfig Studio already installed, is replace them by other png’s in the place where they were installed. It can be different from one installation to other but in the debian package we provide they are at:
/opt/synfig/share/pixmaps/synfigstudio/.png
In the ubuntu package they are at:
/usr/share/pixmaps/synfigstudio/.png
So it depends on how did you installed the package
-G