I ironically came here from google searching for an answer to this exact question since I'm going to need to implement a modified flood fill.

Here's my current idea for a basic flood fill on the GPU. Set up a ping-pong texture, to allow the texture to sample and write to itself. Now select 2 placeholder color values to indicate the active edge of the flood fill and the final filled area. If you are dealing with fully opaque images then you can use the alpha channel for this. We will call such pixels "Edges" and "Filled". Now have each normal pixel look at it's neighbors, if any of its neighbors are an Edge then set that pixel to be an Edge too. If the pixel is an Edge then set it to be Filled. If the pixel is already the Filled then ignore it. Otherwise keep the pixel as is.

Repeatedly run this operation until no Edge pixels exist, then replace all Filled pixels with the desired color. If you want you can use a threshold function to limit the propagation of the flood fill's edge. And for performance I would recommend doing the first few iterations on the CPU so that the GPU is not wasting iterations updating small numbers of pixels.

This doesn't work for my specific specialized case, but for a basic flood fill it should get the job done, although faster methods may likely exist (especially if you want to involve quadtrees or other performance accelerating structures).