When you save your document all project information is preserved, allowing you to edit it at a later date. The publication is saved as a single file with the extension .afpub.
The first time you save your document, you'll be asked to give the project a name and save location. Following this, future saves will overwrite the previous version.
Optionally, you can save a current project as a new project. In this case, the new file will not overwrite the saved version.
Unsaved changes to a document are indicated by [Modified] to the right of the document's name at the top of its tab/window.
Unsaved changes to a document are indicated by [Modified] or [M] to the right of the document's name at the top of its tab/window, and by a star to the right of the current document's name at the top of Affinity Publisher's window.