After updating packages in MikTex, several problems appeared. In textclass.lst all classes are marked as "false".
I had a good working installation of Lyx 2.0.1 with MikTex 2.8.
I decided to install a new package in MikteX today and then run an update using the Package Manager.
Several packages were updated, to their latest versions. Apparently they were all from 2009.
When I opened LyX again, it complained that the book-komascript class was not available anymore.
I checked the document classes in settings, and none of the document classes were available.
He was also asking me for a lot of packages on the fly, that he updated successfully.