The Conversion Bureau never made any sense anyway, but here are some places where it would have made less sense.
Not necessarily worlds where the ponies would lose the fight - just worlds where conversion wouldn't logically work.

Before suggesting a World, read the index to make sure I haven't done it already.

This story is a sequel to The God Empress of Ponykind

A message rings through the Warp: "The Game is broken, only Destruction remains". Celestia hears it, fearing for the lives of her former subjects and those of her beloved ponies. Unwilling to sit idle, she has chosen a dangerous path: return to the Imperium, take up the mantle of Emperor of Mankind, defeat the coming storm, and save Mankind once and for all.

With Twilight Sparkle to aid her, Celestia faces new challenges and new enemies. Her forces are scattered, her people assaulted, and the enemies of Man grow stronger with each passing day.

The Time of Heroes is gone. Now comes the Time of Ending.

Sequel to God Empress of Ponykind. Reading that first is strongly recommended.
Rated T for 40K related violence, but that might change at some point.
Comments contain spoilers. You have been warned.

You're just an ordinary guy, living an ordinary life. But your life changes one miserable Monday, when you arrive home to find an unexpected visitor in your house: specifically, you discover Twilight Sparkle in your bed.

Things go downhill fast.

And she's just your first visitor.

Tags and contributing authors will be added as needed. A couple new chapters will be added daily until the well runs dry. Continuity is overrated, so don't complain about it. It's a thematic collab, not a big budget Hollywood movie where there are never any continuity errors.
Do you want to join? Click here!

This story is a sequel to The Conversion Bureau: Worlds Where It Wouldn’t Work

The Multiverse is a large place, and there are infinitely many versions of Celestia who, for one reason or another, thought it would be a good idea to turn humanity into ponies.

But as the old saying goes, "Anything that can go wrong, will go wrong."

The quasi-official sequel to the comedy fanfic by Sora2455 is here!

Celestia wants to get into her throne room.

A kindergartener wants her to prove she's actually Celestia first.

(A stand-alone, no prior-reading-necessary part of the Triptych Continuum, which has its own TVTropes page and FIMFiction group: new members and trope edits are welcome. )

Now with author Patreon and Ko-Fi pages.

Cover art by EquesTRON.

Just because the two sisters have led Equestria through thousands of years of peace doesn't mean there aren't those who think they can do better.

With a powerful artifact on their side, a group of rebels has sealed Celestia in her palace and stripped her of the majority of her powers. As the last of her guards fall, she hears the pounding on the throne room doors and knows the end is coming soon...

**Featured on the front page on 8/12/15; both surprising and flattering seeing as how this is the first thing of substantial length I've posted here. Thanks all!

**Now with a dramatic reading!

There are two very important things to remember when you cross realities:

1) Every living thing that sets foot in Equestria gets magic if it doesn't have it already.
2) There are three pounds of bacteria living on and in the human body.

Everything goes exactly as expected when two alien cultures meet.

Twilight Sparkle broke time when she got her cutie mark. Now Twilight and Sparkle are sisters from another time. Twilight is hailed as the potentially greatest light magician of all time, and already has a reputation as a hero by the time she goes to Ponyville. This isn't her story, not primarily.

Sparkle is an orphan - her dark magic killed her parents. She lives with her brother in Canterlot's industrial sector because they can't afford anything better. She can't leave either. She's a natural dark mage; while Sparkle won't go mad like Sombra, her reputation is hardly any better. Worse, the law doesn't see her as a good pony.

The fact that the dead don't stay dead around her, or that Thorn - Spike's double - is an undead, soul-eating abomination, are other matters altogether.

(Also has some Slice-of-Life, but fimfiction tags won't let me put it with Adventure.)

Has an ask blog to go with it: Ask Sparkle and Thorn.
Also has a TvTropes page: Split Second Tropes.

Featured on EQD.

Cover art by Swirling Line.

This story is a sequel to The Dresden Fillies: False Masks

It's been a while since the girls have seen their good friend Harry Dresden. Discord escaped, Luna attended her first Nightmare Night, the Royal Wedding was crashed by hordes of changelings, and Pinkie Pie threw a statistically improbable number of parties. They tried inviting Dresden, but between his new job and new apprentice, he always claimed to be too busy. The solution was obvious; if he couldn't come to his friends, they needed to go visit him. Besides, they say Earth is lovely this time of year. What could go wrong?

"No, uh, that's my name. I've got better pickup lines." - Warm Hug, the Crystal Pony/Windigo -

Windigos, the frost spirits of Hearthswarming legends fame, are Equestria's secret peacekeepers tasked with preventing war at all costs, freezing any who dare threaten peace and harmony. Crystal Ponies, on the other hoof, are peacekeepers tasked with spreading Hope and Love through the Crystal Heart. They are one and the same, two sides of the same coin - Windigos in war time, Crystal Ponies in peace time. 'Frostfires', Starswirl once called them - ponies who grow cold in hate, who become warm in Love. With Equestria finally at peace Windigos are few and far between. It had been centuries since the Crystal Empire was last led by a Frostfire Emperor.

Warm Hug is a young blank flank crystal pony, seemingly incapable of the happiness and love required of his kind. Shunned by his kinsman, he spent years wandering. That was until Tirek's invasion of Canterlot forged an unexpected friendship between him and the unlikeliest band of friends.

But their friendship would be sorely tested when an apocalyptic snowstorm strikes all of Equestria and freezes the entire surface world. With Princess Celestia and Princess Cadence frozen solid and Warm Hug accused of high treason, will their Fire of Friendship light the way or will they fall prey to the frost consuming their world? With the world once again in turmoil, never have the Windigo peacekeepers been more loathed yet needed.

WARNING: Season 4 Finale Spoilers.

Now has a prequel - A First Hearthswarming's Tale - the story of Clover the Clever and the Windigo.

Written to the sound of pretty much the entirety of Socratic Brony's Upload List. This guy's music is simply amazing.

Cover Art: Did you know that crystal ponies are difficult to colour? Neither did I. Now I do. All them sparkles. So many sparkles.