After the Exodus from Equestria, Shepard spends some time talking with the crew about the Equestrian refugees. While chatting with Yeoman Chambers, she points out Silver Spoon, who had broken down after realizing that Diamond Tiara, her only friend in Ponyville, was just a projection created by Discord to be an antagonist for the Cutie Mark Crusaders. Said Crusaders are shown forgiving and comforting her.
Early in Shades of Twilight, Silver Spoon is shown to be hanging out with the Crusaders and other foals on much friendlier terms.
Hell, They've formed a new group, the New Equestrian Crusaders along with Silver Spoon
Forty-Two letting Twilight know that she hasn't lost everything associated with her life in Equestria with just five words: "I'm your number one assistant."
Shades of Twilight:
Ditzy Doo takes it upon herself to look after all the "orphaned" foals whose families were actually programs in Equestria.
The way the voter choices play out in the conclusion chapter for Arc 1 is pure heartwarming. After spending such a worrying amount of time with Applejack's labor plan showing virtually no returns, her appeals during the Directors' interview with Emily Wong draws the attention of one of the construction firms who are rebuilding the rest of Tayseri Ward. After hammering out the liability issue, the Equestrian laborers get put to work, and with help from Pinkie Pie's upgrades to the Omni-Hoof (a version of the Omni-tool), they soon end up making progress days ahead of schedule. Even the 'clothes over food' choice is justified when a stallion gets caught up in a fuel line explosion, but thanks to the fabricators Rarity was able to buy with her funding, he was outfitted with heat-resistant work wear that saved his life.
Also, toward the end of the chapter, Twilight has Forty-Two send Shepard an e-mail telling him about the progress New Ponyville has made, just like the letters she used to send to Princess Celestia.
Even though she clearly didn't put much thought at all into the best way to do it, the lengths that Applejack is willing to go to protect her friend Patch is heartwarming.
Forty-Two's flashback to Lady Astrolia's childhood, when he found her trying to use her biotics to move the moon and stars to make the next day come sooner. Just a sweet, innocent snapshot of how things were before the Star Daemon War ruined everything the Equines built.
Meta: after the author seemingly abandoned the fic on a cliffhanger, their editor 2dextreem stepped up and released a final chapter to wrap up the current story arc and gave loyal fans some closure.