Hi there,
I noticed that when about 12 prefabs are connected together like a staircase (picture below), it seems like the saving process breaks down
There's a serialization depth setting which could potentially cause this (Tools > Easy Save 3 > Settings > Advanced Settings > Serialization Depth), in which case increasing it should resolve the issue. However, it sounds like you don't actually want to save the children per se (see below).
If it is possible to spawn specific prefab and adjust, its local rotation, the material of its child, and whether it is active. Sorry if the question is wierd but I tried to look for guides in the documetation and youtube and I am still confused.
If you want to save a prefab but not save anything about it's children, you can do so by disabling
Save GameObject Children in Tools > Easy Save 3 > Settings. The children will still be spawned as they're part of the prefab, but they will keep their default values as nothing about them will be loaded.
All the best,
Joel