The end of the article is incorrect. Yes, the Rock Island Railroad lost the use of the top level of the Government Bridge in 1980. However, the trackage is still used as part of the Iowa-Interstate Railroad line from Omaha to Chicago.
There has been in place for some time, a lease of the trackage by the owner (US Govt/Rock Island Arsenal) to the Iowa Interstate Railroad.
This is by far the most in depth article I’ve ever seen on the history of the legal wranglings over the bridges.
The lawsuit is perhaps most famous because of Abraham Lincoln being the attorney for the railroad. However, the whole history of the transcontinental railroad is key to the development of the US. Jefferson Davis wanted a southern route. Industry, concentrated in the north, wanted a northern route despite the problem of the Rocky Mountains.