web site configuration lost with os x server 4 upgrade

When upgrading form OS X Mavericks / OS X server 3.2.1 to OS X Yosemite / OS X Server 4.1, I lost all my website configurations.

I'm running different websites under OS X server 3.2.1 (rouncube, static html, wordpress,...) and when upgrading to OS X Server 4.1 I lost all the websites config. I only have the standard 2 websites secure and not secure.

Any idea of the cause of the issue and how to solve it?

Thanks

P.S. when configuring a new site using php. I get an error 500... as if round cube/wordpress were not compatible anymore.