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The Gazebo that ROS uses is the standard third-party library with a ROS wrapper around it. When you re-make Gazebo, you're pulling down the original source version from the Gazebo site.

In order to modify gazebo itself, you must create a patch for your changes (as a diff against the downloaded version), and add that to the patches/ subdirectory.

Additionally, you can find and replace the original address in all files with the new address on your local machine, then eliminate all autogenerated files with make clean or the like. You might also need to remove some conflicting lib files. After that, you should be able to make it fine.

I believe that the default makefile that CMakeLists.txt invokes is Makefile.gazebo.tarball, so that's where I would change the address first if you're going with this route. Just be aware that doing this means that any updates to Gazebo will overwrite your changes. As such, the patch method is safer.