Hey! Thank you for the suggestion, we'll keep it in mind. In the meantime, if it helps, you can use the color-filler and color-replace tools on the entire image, not just the visible area. Check the small panel of the sprite editor after selecting the color-filler tool in the tools column on the left. Let us know if this helps!

Sorry for late answer, but color fill/replace tools are not useful in my case.

So what's my case: I wanted to swap two sprites in sheet. So how did I imagined this:

1. Select the first sprite with Ctrl+A
   
2. Copy it with Ctrl+C
   
3. Paste it on blank space with Ctrl+V
   
4. Copy the second sprite with Ctrl+C
   
5. Paste the second sprite to first sprite space with Ctrl+V
   
6. Cut the first sprit from previously blank space with Ctrl+X
   
7. Paste the first sprite to second sprite space with Ctrl+V

How did it turned out:

1. Select the first sprite with mouse
   
2. Copy it with Ctrl+C
   
3. Paste it on blank space with Ctrl+V
   
4. Select the second sprite with mouse
   
5. Copy the second sprite with Ctrl+C
   
6. Select the first sprite area with mouse
   
7. Clear the first sprite area with Del
   
8. Paste the second sprite to first sprite space with Ctrl+V
   
9. Cut the first sprit from previously blank space with Ctrl+X
   
10. Select the second sprite area with mouse
    
11. Clear the second sprite area with Del
    
12. Paste the first sprite to second sprite space with Ctrl+V

Clearing area before pasting is fair enough, but having to select the sprite with mouse even when you are working with whole sprite is not really convenient. Color fill/replace tools will not help in copying/cutting the sprite.

Hello again, and thank you for responding and providing an example.
This is definitely something achievable, and we will keep it in mind for future releases. At the moment, our focus is primarily on the Launcher and Campaign releases, but we would certainly like to incorporate some quality-of-life improvement features.
Thank you for the suggestion!