Hmm... perhaps something like this, might work. I haven't tested, so I apologize in advance for any errors this may have. Tell me if it works!
//Place in 'system.vc' or an #included file.
//Fades a layer into nothing...
//Unless I screwed up, in which case it does the opposite.
//The argument 'z' is the layer on the map that you want faded.
//Call this function from a map event when you want to utilize it.
void FadeOutLayer(int z)
{
int fade_time=timer+200;
while(timer<fade_time)
{
Render();
layer[z].lucent=100-((fade_time-timer)/2);
ShowPage();
}
}