Both Backshop and SD60MAC9500 have the story and route of the Michigan Air Line Railroad partially correct. A good source for a history of the MAL is in the late, great Don Meints' book, "Railroads For Michigan". The MAL never operated as one company from St. Clair to Elkhart. Nor did it go to Elkhart - the west end of the MAL went from Jackson to Niles. Three Rivers to Niles was abandoned around the early 1940's. (A little piece of the through line between Three Rivers and Niles is still left in Three Rivers). Trains using the former MAL between Jackson and Three Rivers got on or off the former LS&MS (nee Michigan Southern/Michigan Southern & Northern Indiana) at Three Rivers and used that line to get to and from Elkhart, but that portion was never part of the MAL or the Michigan Central. It had always been part of the LS&MS and its predecessors. Soon after it was built, the western part of the MAL fell under the lease control of the MC and was eventually merged into the MC in the 20th century. At the time of the 1870's lease to the MC, the portion to St.Clair was not even connected to the western part of the MAL and in Mr. Meints' words, "its owners lost interest in the disconnected part on the eastern end."
I don't know what the procedure was before Elkhart Yard was modernized in the late 1950's, but to go along with that modernization the former MAL between Jackson and Three Rivers was upgraded with TCS installed on it around 1958 as Niles Yard was downgraded to go along with the Elkhart Yard improvements. MC traffic destined for western connections was then taken to Elkhart instead of Niles. (My eldest daughter's high school science teacher turned out to be the son of the NYC (MC) Division engineer at the time of the upgrade and spent his summer off from college in 1958 working as a trackman on the upgrade. I confess that I spent one parent/teachers night with him talking about the railroad).
The Air Line was one of the parallel routes of Conrail (the Panhandle from Columbus, Ohio west is another good example) that Stanley Crane quickly shut down after his 1981 Conrail arrival. However, Elkhart and west traffic out of Detroit after the Air Line was shut down was still using the original MC to get to Elkhart via Kalamazoo in the middle 1980's in the form of DREL out of Rouge Yard and DWEL out of Livernois. The Air Line was abandoned because Mr. Crane did not see the need for two separate parallel main line routes - not because the Detroit Elkhart traffic was sent to Toledo. What Mr. Crane did do with the Detroit eastern and southwestern traffic was to close the Livernois hump, downgrade that yard and sent that traffic either to Toledo Stanley to be switched or on through trains operating via Toledo.
Backshop
Probably changing traffic patterns. Here in Michigan, we had the Michigan Air Line. It ran from Jackson down to Elkhart, IIRC. Conrail decided that all westbound traffic should go down to Toledo from Detroit, instead of using the Michigan Central. The Air Line was soon abandoned.
Not only that.. The MAL actually ran all the way from Elkhart, IN to St Clair, MI. There was a carferry operation from the late 1800's to the turn of the century from St Clair to Courtright, ON. This ferry operation connected to a CASO Line which branched off from the main at St. Thomas, ON.
Later in the 20th Century GTW operated the line from Jackson, MI to Richmond, MI. GTW kept the section from Pontiac to Richmond. Most of the portion of the route from Jackson to Wixom would get abandoned in the 1970's. A small section from Wallad Lake to Wixom would be kept by COE Rail to operate the dinner train.
GTW kept the Pontiac-Richmond portion. This was known as the Romeo Sub. GM at the time still had quite a bit of assembly in Pontiac at its Woodward Truck Plant and Bloomfied Hills Assembly. As well the Romeo Sub served Ford Romeo Engine plant.
CN would abandon sections of the Romeo Sub throughout the 1990's. With the Sub entirely abandoned by the year 2000. As you know being a fellow Michigander GM eliminated all assembly in Pontiac and Bloomfied Hills. Romeo Engine now ships mostly by truck. However some loads still go by Triple Crown. Those TCS trailers go from Melvindale, MI to Voltz YD in KCMO. Destined for Ford's Claycomo Plant in KCMO which also assembles the F-150 along with its Transit Vans.