The below code snippet shows how to change name of named boundary. The code changes name of first named boundary from the collection.

//Required References
using System;
using System.Diagnostics;
using Bentley.DgnPlatformNET;
using Bentley.MstnPlatformNET;

public void ChangeNamedBoundaryName()
        {
            try
            {
                //Get active DGN
                DgnModelRef dgnModelRef = Session.Instance.GetActiveDgnModelRef();
                DgnFile dgnFile = dgnModelRef.GetDgnFile();

                //Get all models 
                ModelIndexCollection modelIndexCollection = dgnFile.GetModelIndexCollection();
                foreach (ModelIndex modelIndex in modelIndexCollection)
                {
                    DgnModel dgnModel = dgnFile.LoadRootModelById(out StatusInt status, modelIndex.Id);

                    //Get Named Boundary Collection from current DgnModel
                    NamedBoundaryCollection namedBoundaries = new NamedBoundaryCollection(dgnModel);

                    //Iterate the Named Boundary Collection
                    foreach (NamedBoundary namedBoundary in namedBoundaries)
                    {
                        //Change name of first named boundary from collection
                        namedBoundary.Name = "SampleNamedBoundary";
                        namedBoundary.Save();
                        break;
                    }
                }
            }
            catch (Exception ex)
            {
                Trace.WriteLine(ex.Message);
            }
        }