To change one color to another you need to make color(s) you want to change transparent, then specify background color and remove transparency.
Example*:
ICPCL.exe -convertto jpg "C:\Source Images\*.*" -dest "C:\out\" dither:no -oper ReplaceColor src_color:"r:255,g:0,b:0,a:0"
ReplaceColor dest_color:"r:255,g:255,b:255,a:255" src_color:"r:0,g:255,b:0,a:0" dest_color:"r:255,g:255,b:255,a:255" ReplaceColor src_color:"r:255,g:255,b:255,a:255" dest_color:"r:0,g:255,b:0,a:0"
In this example we changed red and blue color to green.
* This example works the same way with other support formats.