there are following ways how can accomplish that (it all depends on how the image is composed):
if you know the part you want to keep transparents starts at 0x0 You start by removing all transparency with something like http://www.imagemagick.org/Usage/masking/#remove
and then re-add the transparency using flood-fill starting at 0x0 http://www.imagemagick.org/Usage/masking/#bg_remove
You have more control over whats going on by using a transparency mask:
then you start modifying the mask (which is now only black/white), by coloringusing floddfill starting wiht 0x0 (i.e. with blue), replacing the black with white and then replacing all blue pixel with black (for color replacement see http://www.imagemagick.org/Usage/color_basics/#replace)
# the mask
convert original.png -alpha extract mask.png
convert mask.png -fill blue -draw 'color 0,0 floodfill' mask_blue.png
convert mask_blue.png -fill white -opaque black mask_filled_blue.png
convert mask_filled_blue.png -fill black -opaque blue mask_filled.png
# change transparent to skyblue
convert original.png -background skyblue -alpha remove -alpha off original_nontransparent.png
# apply the modified mask
convert original_nontransparent.png mask_filled.png -alpha Off -compose CopyOpacity -composite final.png
Note that this techniqe works only moderatly well with half transparent things (see http://www.imagemagick.org/Usage/antialiasing/#floodfill ).
For better results with half-transparency you might want to use different methods to "fill" the mask. You would i.e. just draw a shape instead of the two fill operations on the mask:
convert mask.png -fill black -draw "circle 40,80 60,60" mask_filled.png
this will fill the center, but keep the half transparency intact.
if you know the "center" is always trnsparent, you could also floodfill from the center.
Hope this helps