For security reasons, Oracle now recommends (and might obliges one day) to include the APPLICATION.JNLP file of the applet in its main jar. That's the main change I performed in Sweet Home 3D applet version 4.4 (see diff with version 4.3 here).
So, if you want to change the libraries you need in your version of the applet, you'll have to update the file SweetHome3DApplet.jnlp found in deploy subfolder, then update jnlp_embedded parameter and jars variable in SweetHome3DApplet.html.