Your SH3D installation should not be in the /home/.eteks folder, this folder is for your personal additional files like furniture you are adding or plugins.
My SH3D installation e.g. is in the usr/share folder and there in a separate folder for each version of SH3D. In this way, I can test the latest version first before I delete the old one.

I also like to keep several versions around. I use a symbolic link such as Live or Latest to point to the one that desktop users should be using.

I also like keep the install in a filesystem that is separate from the OS (to avoid OS upgrades clobbering anything). Either under /home/local or /usr/local depending on the organisation of the available drives.