As you sure noticed when you watched the Finale, some ponies were missing in it:

Our three Cutie Mark Crusaders.

I strongly reckoned with it that they would be the ones who save the day and who defeat Starlight Glimmer in the end, because of their special cutie marks and the mysterious power they hold, which caused the magical outburst when their cutie marks appeared. But then everything came different and they did not even have a real role in the Finale.
Still, they must have been in the alternate timelines somehow. And it's very suspicious that we haven't seen them anywhere.
Applebloom wasn't on the farm in the Crystal Empire War timeline, none of them were in Zecora's hideout in the Everfree Forest in the Chrysalis timeline and they didn't seem to be in the castle in the Nightmare Moon timeline.
What do you think happened to them in the several timelines?
I have to say, after realizing that they wouldn't defeat Starlight Glimmer, I was rather glad that we didn't got to see them in the alternate timelines. None of these timelines were safe environments for three little fillies and who knows what terrible things the war, the changelings or Nightmare Moon's reign did to them. There are lots of things they could have suffered from in dangerous environments like this and my heart couldn't bear to see such horrible things happen to them.
But maybe they were safe somewhere? Maybe they even played their own part in keeping other ponies safe?
And what is with their cutie marks? Did they still got them the way they did? Did they get different cutie marks or maybe no cutie marks at all due to the changes in the timestream?
What do you think were they doing in the alternate timelines? Tell us your theories!

4890150 Maybe I'm morbid, but my guess is they either got killed off or taken prisoner in the alternate timelines.

4890150 I remember they met a Diamond's party after Nightmare Moon's attack.

Here's what I'm thinking...

Nightmare Moon World...
Applebloom endless work on the farm to make the finest apples for their ruler and possibly eats little.
Sweetie Belle in a comfortable house seeing as Rarity works for the lungs leader, but she probably doesn't bond well with her.
Scootaloo with her parents and is a citizen of the town living a normal life, but she's teased due to her lack of flying and possibly feels a little sad.

None of them know each other...

Discord land.

Each of them are in complete nonsense and can't talk sense into their respected role models if they're harmed. They possibly are also unfriendly to each other since Discord could screw them up too.

Sombra's world.

Hidden from the war, but helping the cause.
Applebloom works like Applejack.
Sweetie Belle is Rarity's assistant or distant sister.
Scootaloo, if she still knows Rainbow Dash in a way, works to become a soldier like her.

Chrysalis...
Their working to keep things safe just like everyone else, but they may have been kidnapped at some point, just to haunt the village.

Flim Flam world...
Applebloom gone or works for the two, since her family had beef with them.
Sweetie Belle probably somewhere safe with Scootaloo.

That's my guess.

4890150 I thought I was the only one to notice that detail missing and to be honest, I'm rather glad that they did not dive into them because I'd be afraid as to what happened to them in each of the timelines...

4890178

4890332

Yeah, that's exactly what I meant..... I couldn't write it out what might have happened to them in the startpost, as my heart already couldn't bear to do just that, so I left it vague.
I wouldn't have wanted to see that either.

4890201

Sweetie Belle in a comfortable house seeing as Rarity works for the lungs leader, but she probably doesn't bond well with her.

I can see that very well. Rarity is different in this timeline ("I don't socialize with dragons!"), so maybe she isn't the generous spirit we know her as.
When Nightmare Moon took over and nopony could stop her, she decided to side with her, as she knew this would be her only chance to live in the glamour she's used to, so she joined her side and became her servant.
Sweetie Belle became resentful because of that, cause she rather sacrificed Equestria to live a glamorous life as a rich pony, than trying to stop Nightmare Moon. This drove a wedge between them and she started to hate Rarity.
Maybe she joined a group of ponies who try to find the Elements of Harmony, that were hidden by Nightmare Moon in an unknown place, and becomes the new Element of Generosity in place of her sister.
Meanwhile, Rainbow Dash works for Nightmare Moon too, as one of her guards, but for different reasons.
Nightmare Moon darkened the sun for all times, which let all crops die and no new ones grow anymore, so a famine broke out quickly and many ponies died because they didn't have food anymore. Finding new food got harder day after day and Nightmare Moon was using this to her advantage.
Using a spell, she let special, edible plants grow that didn't rely on sunlight, but she kept them guarded in the garden of her castle and only those who obeyed to her were delivered with those plants. Everypony who didn't follow her or tried to rebel against her was immediately cut off the supplies and left dying.
In order to save Scootaloo and prevent her from starving, Rainbow Dash made a hard decision: To join Nightmare Moon.
But since she knew that Scootaloo would be against it and never agree to that, she had to pretend that she has gone evil and become a true follower of Nightmare Moon, and so she did and forced Scootaloo to go with her, pretending that she wants to make her a follower of Nightmare Moon too.
Scootaloo didn't understand the world anymore, why was her big sister suddenly not loyal to Equestria anymore? Since Rainbow Dash never told her the truth, she can't see that Rainbow Dash has given up her loyalty for Equestria to be loyal to her.
I think that's what happened to Scootaloo.

Hidden from the war, but helping the cause.

Running out of soldiers, Celestia had to make the decision to also draft the foals of Equestria as soldiers and therefore, declared that every filly and colt had to leave their respective hometowns and leave for a military base in southern Equestria to be trained for the war against King Sombra.
Families who didn't want to let their foals being drafted into war were forced to it and Celestia sent guards to take their foals away to the base.
Applejack, Rarity and Rainbow Dash didn't allow this, though, so they made a plan together and hid Applebloom, Scootaloo and Sweetie Belle somewhere safe. Now they are there, trying to live a normal life, but constantly afraid of being found in their hideout and drafted into war too.
I have a feeling that's what happened to them in King Sombra's timeline.