Big Site !!!!

Hi there, I have another question: We are managing a rather large web site. There is a stangard navigation on the entire website. When our client requests a change to this - it is a monster to change because we have 300 files to change individually and upload. I recommended SSI's but was informed that this would cause problems for something as big as the DHTML navigation in terms of speed. My next suggestion was using PHP and functions to make lif easier. However the problem is that the site is already submitted to search engines and I have been told that many search engines do not look at PHP code. Does anyone have any suggestions about this. Any help would be kindly appreciated. Thanks Abe