WMG / The Conversion Bureau: Not Alone

Lyra will become an Expy of The Joker.

Being cast out from the herd and hated by everyone is probably enough to qualify for a Very Bad Day.

The events of the Conversion Bureau and war will free Discord.

And he will complement the ponies of Equestria for all the Chaos that they cause and that he couldn't have done it better himself. which will horrify them all.

After the epilogue, the full ramifications of the potion will hit Equestria.

Celestia's intentions were obvious. But what about her unintentional actions? The fact that there are quite a few ponies that have the ability to manufacture the potion will have quite an impact on all the Equestrians, not just the ponies. There are two targets the Ponies can use the potion on.

1. The Non-Ponies The Griffins, the Diamond Dogs, the Buffalo, the Dragons, and the Zebras. What's to stop some idiots with good intentions from trying to 'rescue' the other species? If the events of "Over a Barrel" could have been solved by ponification of the Buffalo, don't you believe that some ponies would have done so instead of negotiating? Or against the meat-eating Griffins or scary Dragons? The problem is that Celestia cannot pardon such a PER equivalent without making it look like government sponsored assassination, which easily borders on act of war. And even if she disapproves of it, some ponies might easily see it as "Celestia hasn't forbidden it" and do it anyway. Even Changelings would join in on the action to defeat the Ponies. I would cheer the Nazis if they fought the Draka, so even Chrysalis would get my support if she went up against TCB-Equestria.

2. Other Ponies. This actually ties in with what Twilight realized about the potion. A Pegasus that might end up winning a flying competition or even just has a better job ends up as either an Unicorn or Earth Pony, thanks to jealously. A Unicorn that does well in magic can lose it because of the same reason, or envy. Hell, even the Earth Ponies might end up being targeted because of a Unicorn/Pegasus thinking they want to give their friend a gift beyond their strength, or even voluntarily for the same reason. Even if it doesn't change their form, what happens to the personality could be enough to break them. Why, it might even change their Cutie Marks. Instead of CMFIS, you have CMDIS (Cutie Mark Dissociative Identity Syndrome), where the pony is caught between doing both of their Cutie Marks, in a way that looks like Cutie Pox-lite, but still horrific. A bit of Moral Myopia as the ponies realize that losing the range of emotions and becoming a newfoal is not what they want happen to them.