In a project of mine I have a window containing 2 text layers (like header and footer), and in between I have the QR layer. I always had a valid QR displayed upon creation, but it always became invalid (ie. no reader could read it) when I tried to update it (using qr_layer_set_data).
After a bit of playing I realized that "clearing" the GRect first helps. My patch basically fills the GRect with a pre-defined BG color, and then sets the fill color back to "black". Unfortunately I could not find a call to read the fill colors, so therefore I defined them in the header. I don't like this part, but well, works for me..

I really like the idea of using a new layer for this purpose. Thank you for this great lib!!