Oh my god the problem is fixed !!! :-)
It was the APC Cache. We turned of caching and the site is working. Turning on cache ->
site is not working.
For me this is very strange APC is only a bytecodecache for PHP Files right? Thoose
problems should never ever happen!
Maybe someone open the files while it was not working and after we fixed the problem the
cache still says the file is not there.
Does someone know how to empty the apc cache?