You need to make so that your entire game board can be re-drawn or destroyed at will.
Destroy your entire game board, and have the window resize to 256x256 or whatever avatar size you want. Then do the snapshot. Destroy the snapshot elements, and re-size window to original dimensions, and re-draw the game board.
Some things that will help:
Use wait. If you instantly try to re-draw after a window resize the X and Y cords will be wong on random objects. Give it a second or 2 to cool down, then try re-drawing you window elements.
use the Anchor behaviour. Sometimes this is helpful to keep your objects where they belong. Most of the time it does not though, so re-drawing your entire game board and putting things where you need them seems to be the best way of doing things.
If you can not keep the elements in focus, try the system > Scroll to, to correct the viewport positioning.
Positioning things after a window resize is more of an art than a science it seems.
Screenshots could be really useful. I wish we could get a snapshot-under-sprite so we could easily snapshot small regions of the screen. I doubt node webkit can do this though.
If you are trying to do this in a web-browser the rules change completely it seems.