T-1000s can feel emotions and are capable fo defying Skynet’s orders(hence why Skynet stopped making them). What would make an interesting plot line would be if Fluttershy was a t-1000 sent back to kill twilight. Fortunately she was sent back 20 years before she was supposed to arrive. As a result she decided to integrate into pony society and take up residence in Ponyville to wait for her target’s arrival. During those 20 years her mind and personality developed, and she eventually found she enjoyed her new life. As a result she abandoned her original mission and now lives a normal life.

Flutterminator

Considering t-1000s are capable of true free will and are able to defy skynets orders  
This seems like a situation for the magic of friendship or something

@Vree  
I made that comment as a response to (Future) Twilight saying “I was assigned to Lyra’s Training Unit”

@Revan0123  
WHERE IS SHE

Oh Lyra…

6th panel Giant mouth