Hello all again,
I have fixed it. The problem seemed to be that in my last update, ispconfig have updated the script (webalizer.php in this case) and not the ispconfig tables in the DB. So webalizer.php was checking in the table for a new field in the table isp_isp_web called webalizer_stats to have value 1, but that field was not in my table. So just added it, filled it with 1's and it worked!
Then I have manually created temporary symbolic links of /homw/www/www.mysite.com/log/web.log to the months I lost... and run webalizer again...
logs.php restored the links after that (I previously have deleted them all)
Any question? just post...