Fireworks can batch process...
Unsure about how you're going to do the actual recolour, but you can select all your PNGs to convert to 4-bit in Fireworks, set export to 16 colour PNG with alpha channel.
Once you have all the 4-bit PNGs, use a batch file to run it through GimConv with the "-bpp4" flag set.

Then, dump the osk RCO with Rcomage, not converting GIMs, and simply replace the GIMs in the dump with the ones you just made, then compile.

Hope that helps.