Created a transparent "test_template" just like yours, Here's the path: "C:\Users\username\AppData\Roaming\NCH Software\VideoPad\EffectTemplate\test_template.vfc" You should be able to delete there.
The effect showed up below most others, in the TEMPLATES section. Clicking on it applied only that effect to the clip - there was no "fade in/out." "Clear Mask" was also listed, but it didn't appear to alter the effect.