But then if something else goes down
Which it will one day, unless your code is a lot better that mine 
All such systems should be fail safe or fail to manual. How will you ever sell the house with an Arduino controlling everything?
I really don't know how other people get around this, they either don't care or have thought of something clever, I should know as I used to work in building control :), but a long time ago.
Rather than having the Mega decide about every light switch I can see a module where the button toggles a relay, one pole of the relay is an input to the master controller so it knows what's going on. The master can also toggle the relay remotely so when it is working it can automate the process but nothing actually relies on the master.
Is there any other project similar to mine somewhere ?
There would have to be, home automation is one of the most popular subjects around here I think. That said I don't know where to look.
Rob