Hey there!
I have this lovely hierarchy under a collection, and i have those collection instances of the pinky one.
After i make an instance real (Make Instance Real)
blender loose all the parenting:
Not to speak, if i have items in another collection (for example Cutters) then making instance real not duplicating the items in those collections.
I guess if an item has a modifier that contains an object reference (like booleans, mirror ect), then code should make them duplicated during the “making real” as well as the items are in the master collection since they are part of the referenced item via modifiers.
So is there a way at least keep the parenting please? 
I know, GroupPro