Reply To: Changing the geometry in existing case

[Rob]

Non conformal is the term used when you have disconnected mesh that's then connected in Fluent using an interface. As you're using internal/interior that's not the case. Assuming the various holes are labelled internal surfaces you can switch to wall in Fluent's boundary conditions which ought to avoid the need to go back to meshing. 

If you are removing any surfaces you may need to check what reports are linked to the old faces. If you delete those (look in Report Definitions for "invalid") the solver should run.