assume you have installed LSWS in /usr/local/lsws
run install.sh to install 4.0.4 to the same directory - /usr/local/lsws
it'll prompt you to upgrade or not. just type "Yes"(following the instruction). then it's an upgrade not an fresh installation.
Just have a try, it won't break anything. after the upgrade, you'll see 4.0.4 in the admin console, and can switch between 4.0.4 and previous versions as you like.