How to diagnose DNS virtual domain 404s

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http://serverfault.com – Until a few days ago I was hosting a single domain on my Server. Now I've added a second domain via apache virtual hosts. Both domains are name based and hosted from the same IP. Now my logs show me that some relative paths are called on the new domains application that obviously belong to the old domain. It seems that all these calls come from searchengine bots and I can still access the two pages without a problem. So there is no real damage done for endusers. But I'd like to diagnose the problem. I'm a fairly good programmer but I don't know much about administrative tasks. Because of t (HowTos)