When checked Regenerate Scenario Before Running checkbox, the target scenario's Material Flow network is regenerated from the latest active data immediately before the engine runs, equivalent to running Auto-Generate followed by Run Material Flow, in one step.
New item-location links, new product introductions, and sourcing changes introduced by a data import don't automatically appear in a scenario's Material Flow network. Checking this option picks up all of that latest data before the engine runs, without needing to manually re-run Auto-Generate first.
The official base scenario is system-managed and not intended for direct manual editing. Planners continue to create and work in planning and working scenarios derived from it, rather than editing the official base scenario's network diagram by hand.