I'm running a variation of Hoard of the Dragon Queen but due to the fact I'm a broke college kid I'm running it via PDF.

Its more of a homebrew version than the strictly following books in an attempt to spice up what DnD Players have dubbed the 'duller' book in Tyranny of Dragons.

Players went to a Cultist camp to retrieve food and a Blue Dragon's Eggs. I decided to make it interesting reworked the Hatchery from the book to be a food storeroom and 3 Sealed stone doors depicting a Black, Red and Blue Dragon breathing their respective elements.

Immediately my players set about opening all 3 doors instead of the one I planned them to open and came up with nifty solutions to the puzzles I pulled out of my ass so I had to reward them.

I gave them 5 Blue Dragon Eggs, 6 Red Dragon Eggs and they discovered a Black Wyrmling cuddling the bones of its dead siblings. I established earlier that the sealed doors forced the Dragons into a Survival of the Fittest situation.

The Dragon Pact Sorcerer immediately rolled to feed it and tame it, Nat20. I rolled with it and decided I wanted to explore the Nature v Nurture argument with my players while they attempt to raise it.

Then my Druid decided he wanted to try and release one of the Blue Dragons and used Shocking Grasp to force it to crack. Again Nat20, so I rolled with it. It opened and the Blue and Black started playing together.

They were seriously hurting after fighting some animated statue in the Black Dragon Room so I decided to give them a break. They devised a well thought out plan to escape with the food, eggs and two wyrmlings and I ended the session before I did anymore damage to myself.

How do I go about taking this away from them seeing as this puts them on an entirely different CR scale? Currently planning for the Blue Dragon to swoop in and recover its Eggs and Baby as planned from the beginning.

But what should I do with the Red Eggs and Black Dragon?

Edit: Thanks Everyone for the Advice! I'm not going to take it all away at once but more gradually depending on player choices.

The Wyrmlings aren't going to be pets but more NPC companions with individual loyalty scores and 'training' them will not be easy.

The Eggs will be taken away slowly depending on player choice. The Blue Eggs are gunna go with the Adult Blue they promised to return them to.

The Red Eggs will stay with them for now making them a target of Cultists and a Dragon Hunter organization.

The Blue Wyrmling will either stay or go depending on their attitude toward it before they re-encounter the Adult Dragon.

The Black will be a hard fought companion that will barely listen until they develop a decent Loyalty and if not properly cared for will flee in the night.