Renaming a document or folder is possible through a variety of means within GoodNotes 5, whether you want to change the name of an existing Notebook or you've changed the contents of a folder and want the title to reflect that.
To rename a document or folder, please tap on its title in the library view to bring up more options. Then tap the title field to edit the name.
This above method of changing the file name works for the tile-based view of the documents, but not for the list-based view. For the list-based view, press the downwards arrow located on the right-hand side of the document (as seen below). This will open a similar pop-up window to the one above, allowing you to re-name any notebook or document.
Note: You can also rename a document while working on it by tapping its title at the top!