But now I have another problem. I am in sandbox of google. Because there are nearly 2000 sites spam linking to a subdirectory (to a php file) of my previous site…. These links are not valid for my new site, but they still are on the internet. And google thinks my site is suspicious…

1- Did you experience the same?
2- What do you suggest me to get rid of all those spam links targeting un-living subs of my domain?

If you don’t make a ton of changes, just backup your template one time, then create or download a script to email you a database dumb every couple days.