If you turn on Auto Trim Trailing Whitespace in the Extra menu then EditPad Pro automatically trims trailing whitespace from lines that you have edited. This happens when you move the cursor away from the line.
Turning on this option does not trim whitespace from lines that you don’t edit. Any trailing whitespace that was already in the file when you opened it or that you added before turning on Auto Trim Trailing Whitespace remains in the file until you edit those lines. If you want to remove all trailing whitespace immediately, use Extra|Trim Trailing Whitespace. Then you can turn on Auto Trim Trailing Whitespace to keep the file free of trailing whitespace.
You can turn on Auto Trim Trailing Whitespace by default by ticking “trim trailing space” on the Editor page in the file type configuration.
Extra|Trim Trailing Whitespace