It can be quite confusing & annoying when a “small” change is made to a a network definition (one “tiny” node or edge is added or deleted) but he resulting layout is unrecognizably different.
Possibly the layers feature (FAQ | Graphviz) can help.
Layers can definitely help preserve consistency in alternative networks (“what if”) and can also help when presenting changes going “backward” in time.
Here links to layers usage: