It won't happen overnight.
[quote name='The Tool' timestamp='1364544578' post='158924']
It won't happen overnight.
[/quote]
The problem with Google webmaster stats is apart from them being wrong all the time, but that doesn't matter if Google uses them to rank your site, the data they show you is incomplete and out of date. In general you are looking at 2 weeks to 2 months for any changes to show up at all.
I wouldn't say the stats are wrong. I have a nice list of products that are no longer in the site but not one url contains /index.php.
They are dated but that is just how Google operates. It seems Google finally gives up on them after about 3-4 months.