I don't know of any slicing software that does that, so I think your best bet would be to load the generated G code into a text editor and scroll through until you find the Z move that changes to the Z height of the layer you want to change (just do a search for "Zxx.xx" where "xx.xx" is the height of your colour change). Then you should copy everything before that point to another file, and everything after that point to yet another file. Print the first file, then without homing, change the filament and then print the second file. You could add a line or two at the end of the first file to get the head out of the way so it doesn't melt a hole in the part while you are changing filament, and a line in the second file to move the head back again.
Dave