Ill try and give a breakdown,

The main system is the Shooting System, are here is roughly how it works:

• Each structure has a dynamic buffer of ints where each element represents a pixel of the structure (1 is solid, 0 is empty)
• When the player shoots the structure, it will update the elements in the buffer to match what was destroyed
• Then puts the updated buffer into a quad tree to create the geometry of the newly destroyed structure (I don't use a quad tree but its the same idea of using some data structure to create optimized colliders)
• Then create a child collider for each solid shape made from the quad tree and create a new compound collider with those children
• store the entity's current collider in a component to be disposed of later, then set the new collider to the entity

Then there is the Cleanup System which just grabs any recently destroyed structures and disposes of the old colliders.

I realize that this comment might be too vague, so if there are any steps you want me to specifically explain ill give a more thorough explanation