Some element deletion processes will create invalid, difficult to undo and difficult for some users to diagnose issues when the element is a critical reference element to a separate elements.
Examples include:
Downstream pipes of Directional Elements (Eg. Pumps, Control Valves, Refluxes)
VSP Pump Control Nodes
Control Action or Condition Elements
SCADA Element referenced Model Elements
An extra deletion step suggested may be a warning Dialog "This will delete model elements that are referenced by other model elements possibly resulting in warnings or errors. Do you wish to delete these referenced elements ? -> Yes/No"
Other modules that involve deletion of elements should consider a hard lockout of deletion of the above Eg. Skelebrator should not delete any of the above, and force the user to delete through other means Eg. Only drawing deletion or ModelBuilder deletion possible.