1. Open this image:

2. Open this image:

3. Select all of the second image.
4. Copy it.
5. Paste it somewhere in the middle of the first image.
6. Deselect it.
7. Press delete. (Clear)
GIF

Nothing below where the second image was pasted is cleared to the background color.

Aseprite 1.1.5.7 on Windows Vista 32 bit