@naddel81
Sometimes running sudo apt-get clean might clear up a little bit more space.
You might be able to free up enough space and the re-run that Update All Installed Packages from the RetroPie Setup Script and it might be able to fix itself and start working again like normal. As long as this time it doesn't run out of free space.
If that doesn't work then try Basic Install from the RetroPie Setup Script and if that doesn't work then I'd suggest backing up everything and re-flashing your SD card and starting over.