Select Save Project As from the Project menu to save the current project under a different name. From that point on, EditPad Pro will automatically maintain the project, updating the file you saved it into. Whenever you open new files into the project, or close files, the project is updated. If the project was previously saved under another name, the old project file will not be updated unless you reopen the old project.
You only need to use Save Project As when you want to save an untitled project, or you want to create a new copy of a previously saved project. There is no need to repeatedly save projects under the same name to prevent losing changes like you would do with files. EditPad Pro always saves project files automatically when the state of the project changes as soon as you've saved the project once to give it a file name.
Project|Save Copy of Project As
Project|Rename and Move Project