Additionally, I'm not sure how to achieve the replacement of individual ordinary tiles in GBS. When I try to replace one, all identical tiles get replaced together. This forces me to resort to character sprites. However, the Game Boy's hardware should be capable of achieving such an effect. For example, in "Harvest Moon," using a hoe to till the land replaces each tile individually as it is tilled.
That might be covered in the next update. However, there is this trick I came up with in my game.
I started with a background that looked something like this:
Then I told the game to replace each tile used for "shocked Keeby" with a solid green tile when the scene started. Then I could put it back to the way it was when I was ready to show "shocked Keeby" again. Of course, I could have achieved this same effect using sprites, but I did it this way to make room for more sprites to appear in a row together. It ended up looking like this in the VRAM:
with shocked Keeby: 
without shocked Keeby: 
Maybe you could try something like that if you've got enough VRAM space.