in the manual , I found this :

If the texture had no mipmaps before, modified texture content gets lost when creating the mipmap chain the first time. Thus, create the mipmaps before modifying the texture, and call bmap_to_mipmap afterwards a second time for updating the modified content to the other mipmaps.
This function can not be applied to compressed (DDS), cubic, normal, tangent, rendertarget, or other special bitmaps. If required, create the mipmaps before converting the bitmap to a special format (for instance bmap_to_cubemap(bmap_to_mipmap(skymap)). Creating mipmaps afterwards will otherwise render the special bitmap unusable.

there's a problem with your code there(if you didn't have mipmaps before ) and I do not save mipmaps out to file yet.

I tested by doing pixel operations , followed by bmap_to_mipmap , which destroyed the modifications and results in behaviour you would not want ,if you were planning on keeping the pixel alterations ..

but still , how are you resizing the bmaps to be non square ? I mean what function ?