The Heart wasn't missing. It was still in the Castle.

My Little Pony: Friendship Is Magic - The Crystalling (S06E06)

Title	Season	Episode
Friendship Is Magic, Part 1 (Mare in the Moon)	1	1
Friendship Is Magic, Part 2 (Elements of Harmony)	1	2
The Ticket Master	1	3
Applebuck Season	1	4
Griffon the Brush Off	1	5
Boast Busters	1	6
Dragonshy	1	7
Look Before You Sleep	1	8
Bridle Gossip	1	9
Swarm of the Century	1	10
Winter Wrap Up	1	11
Call of the Cutie	1	12
Fall Weather Friends	1	13
Suited for Success	1	14
Feeling Pinkie Keen	1	15
Sonic Rainboom	1	16
Stare Master	1	17
The Show Stoppers	1	18
A Dog and Pony Show	1	19
Green Isn't Your Color	1	20
Over a Barrel	1	21
A Bird in the Hoof	1	22
The Cutie Mark Chronicles	1	23
Owl's Well That Ends Well	1	24
Party of One	1	25
The Best Night Ever	1	26
The Return of Harmony, Part 1	2	1
The Return of Harmony, Part 2	2	2
Lesson Zero	2	3
Luna Eclipsed	2	4
Sisterhooves Social	2	5
The Cutie Pox	2	6
May the Best Pet Win!	2	7
The Mysterious Mare Do Well	2	8
Sweet and Elite	2	9
Secret of My Excess	2	10
Hearth's Warming Eve	2	11
Family Appreciation Day	2	12
Baby Cakes	2	13
The Last Roundup	2	14
The Super Speedy Cider Squeezy 6000	2	15
Read It and Weep	2	16
Hearts and Hooves Day	2	17
A Friend in Deed	2	18
Putting Your Hoof Down	2	19
It's About Time	2	20
Dragon Quest	2	21
Hurricane Fluttershy	2	22
Ponyville Confidential	2	23
MMMystery on the Friendship Express	2	24
A Canterlot Wedding	2	25
A Canterlot Wedding	2	26
The Crystal Empire	3	1
The Crystal Empire	3	2
Too Many Pinkie Pies	3	3
One Bad Apple	3	4
Magic Duel	3	5
Sleepless in Ponyville	3	6
Wonderbolts Academy	3	7
Apple Family Reunion	3	8
Spike at Your Service	3	9
Keep Calm and Flutter On	3	10
Just for Sidekicks	3	11
Games Ponies Play	3	12
Magical Mystery Cure	3	13
Princess Twilight Sparkle: Part 1	4	1
Castle Mane-ia	4	3
Daring Don't	4	4
Flight to the Finish	4	5
Power Ponies	4	6
Bats!	4	7
Rarity Takes Manehattan	4	8
Pinkie Apple Pie	4	9
Rainbow Falls	4	10
Three's a Crowd	4	11
Pinkie Pride	4	12
Simple Ways	4	13
Filli Vanilli	4	14
Twilight Time	4	15
It Ain't Easy Being Breezies	4	16
Somepony to Watch Over Me	4	17
Maud Pie	4	18
For Whom the Sweetie Belle Toils	4	19
Leap of Faith	4	20
Testing, Testing, 1, 2, 3	4	21
Trade Ya	4	22
Inspiration Manifestation	4	23
Equestria Games	4	24
Twilight's Kingdom	4	25
Twilight's Kingdom	4	26
The Cutie Map: Part 1	5	1
The Cutie Map: Part 2	5	2
Castle Sweet Castle	5	3
Bloom & Gloom	5	4
Tanks for the Memories	5	5
Appleoosa's Most Wanted	5	6
Make New Friends But Keep Discord	5	7
The Lost Treasure of Griffonstone	5	8
Slice of Life	5	9
Princess Spike	5	10
Party Pooped	5	11
Amending Fences	5	12
Do Princesses Dream of Magic Sheep?	5	13
Canterlot Boutique	5	14
Rarity Investigates!	5	15
Made in Manehattan	5	16
Brotherhooves Social	5	17
Crusaders of the Lost Mark	5	18
The One Where Pinkie Pie Knows	5	19
Hearthbreakers	5	20
Scare Master	5	21
What About Discord?	5	22
The Hooffields and McColts	5	23
The Mane Attraction	5	24
The Cutie Re-Mark Pt. 1	5	25
The Cutie Re-Mark Pt. 2	5	26
The Crystalling	6	1
The Crystalling	6	2
The Gift of the Maud Pie	6	3
On Your Marks	6	4
Gauntlet of Fire	6	5
No Second Prances	6	6
Newbie Dash	6	7
A Hearth's Warming Tail	6	8
The Saddle Row Review	6	9
Applejack's "Day" Off	6	10
Flutter Brutter	6	11
Spice Up Your Life	6	12
Stranger Than Fan Fiction	6	13
The Cart Before the Ponies	6	14
28 Pranks Later	6	15
The Times They Are a Changeling	6	16
Dungeons & Discords	6	17
Buckball Season	6	18
The Fault in Our Cutie Marks	6	19
Viva Las Pegasus	6	20
Every Little Thing She Does	6	21
P.P.O.V. (Pony Point of View)	6	22
Where the Apple Lies	6	23
Top Bolt	6	24
To Where and Back Again	6	25
To Where and Back Again	6	26
Celestial Advice	7	1
All Bottled Up	7	2
Hard to Say Anything	7	8
Honest Apple	7	9