OK, I found a way to feed webalizer with the "forgotten" statistics.
The following will go through the access log files for each domain and gather the information in the todays log file. The old logs are deleted (as the information is now stored in the actual log) to prevent running the command twice and dubblicating data by mistake.
find /var/log/ispconfig/httpd -name "*.gz" |while read g; do gzip -fd $g; done && find /var/log/ispconfig/httpd/ -maxdepth 1 -mindepth 1 -type d | while read i ; do rm $i/access.log && cat $i/*-access.log >> $i/access.log && rm $i/*-access.log && mv $i/access.log $i/`date +%Y%m%d`-access.log && ln -s $i/`date +%Y%m%d`-access.log $i/access.log; done
Next time webalizer is running statistics it will consider all available information from the past days. Thereafter everything will run as usual.
( Do not forget to change the option "Incremental yes" in /etc/webalizer/webalizer.conf).