Hi,
if you made a prefab from the objects and don't remove them from the hierarchy they should still be connected,
But if you would remove them and replace them with the prefabs or if you would place them in a new scene the will indeed break.
also if you would create them @ runtime.
Many thing depends on what you do,
Are the GO's Created @runtime?
if so you can store them into a variable or array to communicate with them.
or are you placing them into different scenes?
then you could parent them to a empty object and make that as a prefab.
Maybe you can show some pictures from what you are trying to do