So, Clover the Clever mated with an unknown stallion, generations pass and Twilight Dusk was born. She was the one who, along with 5 of her friends, worked alongside the engines of the S&M, W&S, T&KLR, CFR, H&BMR, SkR and MSR during the time period between the 1850s and 1910s before the 1st world war broke out. The magic coming from Equestria combined with the Magic Railway was what kept them from ageing. When that finally faded away, the new generations continued.
 
It is now Twilight Sparkle and her friends and loved ones that run alongside the CFR, H&BMR, SkR, MSHR, Aresdale and NWR. (Twilight herself is pony leader for the MSHR, Cadence for the Aresdale and Shining for the CFR.) Shining Armor is now married to his beloved Cadence, Twilight and her new beloved Flashy are dating and Trixie has managed to get Blueblood to show good in him and they started dating too.
 
I.N: For Trixie, I think she is Twilight’s and Shining’s long lost sister. How will they find out? Well… it will be in due time.