For those that wants to do something similar, I found a solution: UE4 - Interact with Foliage at Run-time (Cut down trees, remove foliage, etc...) - YouTube
In spite of all the meshes being instanced together, as Shirk correctly said, you can Break Hit Result, and Remove the Instance using the Component and Index from the Hit. For more details, take a look on the video.
Problem solved.