This one is tricky, after searching a YouTube video of someone giving a tutorial on right clicking the project tab on After Effect, selecting “New Composition” for example, this guy already had Comp 1 and Comp 2 created, after clicking “New Composition”, the default name would be Comp 3 immediately so you will have to rename it by the correct number it was perserved to if you want it to perserve the original name but of course if you already had a composition named that, it will not work. Try starting over and pass in each compositions in the order it should be when no other compositions has that same name yet and see if it helps. Not sure if it helps but like I said, its tricky and seems to be no way around to perserve it besides not having a composition of the same name there. Hope you are able to get around this soon and best of luck!