The timeline will continue to show your project edits, even after export, until you close the project and relaunch Videopad, or manually delete all content.
While editing, Save Project File AS routinely, giving it a unique # or name, so as not to overwrite prior saves. Using Save Project Files (no AS) will overwrite.
To Clear Unused Cache Files click the Menu item at the top-left, then TOOLS | OPTIONS. In the window that pops up, click the DISK tab. Do this before starting a new project. Nothing of the old will be left behind.