Update 2022 - With the dissolution of Miller Pipe Organ Company (that were holding the pipework in storage) the pipes were returned to the church loft alongside the organ. Since the OHS convention 1993, the organ (in the late 90s or early 2000s) had fallen apart with the facade falling in on the organ. While this organ was believed to be the origional organ for the Cathedral, most information points to this organ not being old enough to fit the church (an origional organ was "played in 1819" at the first Mass). While this organ was not built till years later. This organ was once home at the Sisters of Loretto, and later was sent back to St. Joseph as many rumors started that it had to belong to us (dates around the same time).
There are many pipes missing, and even only one pipe of a full rank (the Open Diapason) is left. It's unclear whether all the pipes had ever been transported to Miller, if they were lost in storage through the years. The organ sits away and covered since it's fall.
Updated through online information from John C. Ball. -- The remaining pipes are in storage in good hands and in a safe place.
Status Note: There 1993.
Moved from Loretto Motherhouse, Nerinx, KY. in 1985. Origin unknown.