diff --git a/extensions/notebook/src/book/bookTocManager.ts b/extensions/notebook/src/book/bookTocManager.ts
index 7f1a989fbd..2476a8d9bc 100644
--- a/extensions/notebook/src/book/bookTocManager.ts
+++ b/extensions/notebook/src/book/bookTocManager.ts
@@ -343,7 +343,9 @@ export class BookTocManager implements IBookTocManager {
 
 		if (this._sourceBook) {
 			const sectionTOC = this._sourceBook.bookItems[0].findChildSection(notebook.uri);
-			this.newSection = sectionTOC;
+			if (sectionTOC) {
+				this.newSection = sectionTOC;
+			}
 		}
 		fileName = fileName === undefined ? notebookPath.name : path.parse(fileName).name;
 		this.newSection.file = path.sep.concat(fileName).replace(/\\/g, '/');
diff --git a/extensions/notebook/src/book/bookTreeView.ts b/extensions/notebook/src/book/bookTreeView.ts
index c8651a4035..2b0c2596a0 100644
--- a/extensions/notebook/src/book/bookTreeView.ts
+++ b/extensions/notebook/src/book/bookTreeView.ts
@@ -225,11 +225,11 @@ export class BookTreeViewProvider implements vscode.TreeDataProvider<BookTreeIte
 			} finally {
 				try {
 					await targetBook.initializeContents();
+				} finally {
 					if (sourceBook && sourceBook.bookPath !== targetBook.bookPath) {
 						// refresh source book model to pick up latest changes
 						await sourceBook.initializeContents();
 					}
-				} finally {
 					this._onDidChangeTreeData.fire(undefined);
 					// even if it fails, we still need to watch the toc file again.
 					if (sourceBook) {
diff --git a/extensions/notebook/src/book/bookVersionHandler.ts b/extensions/notebook/src/book/bookVersionHandler.ts
index 011e3aa6e5..3548351731 100644
--- a/extensions/notebook/src/book/bookVersionHandler.ts
+++ b/extensions/notebook/src/book/bookVersionHandler.ts
@@ -38,7 +38,7 @@ export function convertFrom(version: string, section: JupyterBookSection): Jupyt
 			divider: (section as IJupyterBookSectionV1).divider,
 			header: (section as IJupyterBookSectionV1).header,
 			external: (section as IJupyterBookSectionV1).external,
-			numbered: !(section as IJupyterBookSectionV1).not_numbered,
+			numbered: (section as IJupyterBookSectionV1).not_numbered !== undefined ? !(section as IJupyterBookSectionV1).not_numbered : undefined,
 			not_numbered: undefined
 		});
 	} else {
@@ -56,8 +56,22 @@ export function convertFrom(version: string, section: JupyterBookSection): Jupyt
 	}
 }
 
+/**
+ * This method is used by JupyterBookSection to convert it's numbered property to
+ * not_numberered.
+ * Or it's used by an JupyterBookSectionV1 to make a deep copy of an object.
+ * @param section The section that'll be converted.
+*/
+function convertNotNumbered(section: JupyterBookSection): boolean | undefined {
+	if (section.numbered !== undefined) {
+		return !section.numbered;
+	}
+	return section.not_numbered !== undefined ? section.not_numbered : undefined;
+}
+
 /**
  * Converts the JupyterSection to either Jupyter Book v1 or v2.
+ * This method is also used to make a deep copy of a section object.
  * @param version Version of the section that will be converted
  * @param section The section that'll be converted.
 */
@@ -68,7 +82,7 @@ export function convertTo(version: string, section: JupyterBookSection): Jupyter
 			temp.title = section.title;
 			temp.url = section.url ? section.url : section.file;
 			temp.expand_sections = section.expand_sections;
-			temp.not_numbered = !section.numbered;
+			temp.not_numbered = convertNotNumbered(section);
 			temp.search = section.search;
 			temp.divider = section.divider;
 			temp.header = section.header;
@@ -84,7 +98,7 @@ export function convertTo(version: string, section: JupyterBookSection): Jupyter
 			newSection.title = section.title;
 			newSection.url = section.url ? section.url : section.file;
 			newSection.sections = section.sections;
-			newSection.not_numbered = !section.numbered;
+			newSection.not_numbered = convertNotNumbered(section);
 			newSection.expand_sections = section.expand_sections;
 			newSection.search = section.search;
 			newSection.divider = section.divider;