The question: What is the most effective way to write a blurb on a story with multiple MCs?

Okay, I get that quite a lot. People have as much as ten POV. Actually, a blurb is a tick easier than a logline. There, you had best get the one for GOT as a blueprint. 

The current blurb I have two MCs, but plan on continuing on to a second book with three. (What, only two? LOL. That's comparatively easy.) Joking aside, I think you do a good job here, by first showing the differences between your sisters, and then bring them together in the third paragraph. That worked for me. I still had some observations. 

First paragraph: 

Two sisters ripped apart by the confines of their kingdom; two souls seeking freedom from a bloody fate.
One was given her father's legacy as a shape-shifter, while the other was long forgotten by the Gods...
Or so she thought.

Feedback on first paragraph: 

It's punchy and certainly provides a hook. From that perspective - a good job. However, I see some issues with logic here and the language is too loose for me. 

Could be rewritten: 

Two sisters ripped apart by civil war/war raging in their kingdom; two souls seeking escape from a bloody fate.
One was given her father's legacy as a shape-shifter, while the other was forgotten by the Gods. Or so she thought.

Second Paragraph: 

Lina was stripped of her titles in order to fight for her future as a Warrior. Grace was given an opportunity to advance herself as a Lady in waiting. Neither wants what their Empire offers them. 

Could be rewritten: 

To become a warrior, Lina had to abandon her previous life/forego her royal privileges etc.

To become a lady of waiting, Grace had to (do what? Show the stakes. At the moment, Grace faces no conflict). 

Neither likes the choices offered by their Empire.  

Third paragraph: 

War is looming over the Empire of Mantiva, with deadly prophecies lingering in the air. One that promises the fall of the monarchy at the hands of an untamed power, and another that promises to see the rule of the Empire's youngest heir. With tensions running high across the continent, the sisters will have to band together in order to survive the dangerous threads of their (something must be missing here). 

Feedback on second paragraph: 

Since this brings together the previous information, I would change the style to be a little bit less abrupt. It works before, but some full sentences will do a better job. 

War is looming over the Empire of Mantiva, and deadly prophecies foretell a dire future.  One promises the fall of the monarchy at the hands of an untamed power. The second predicts the reign of the old King's  youngest heir. With tensions running high across the continent, Lina and Grace will have to draw on their very different skills in order to survive.