How to recover from a messy situation?

[aglien]

Hello all,
I'm in a trouble.
I was using ispcp 1.0.0RC6 but, step by step, it started to working bad and I started to change the /etc/apache2/sites-avaliable/ispcp.conf by hands.
Finally I tried to upgrade to version 1.0.0.
I followed this tutorial:
http://www.isp-control.net/documentation...upgrade:rc
All was fine until I launched this script:
perl ispcp-update
After a while it stopped working with the error: "mysql was gone away".
I changed the mysql server time-out and I relaunched the script.
This time the script stopped simple with "failed".
Now all is very messy. Ispcp is not working.
The server is a production server. It contains about a hundred sites. The sites are working but now is impossible to change anything.

Is it possible to recover all (or somethings) by hands?
Is it possible to transfer the sites, one by one, to another server?
Any hint is welcome.
Many thanks

Enrico