Linux Malware Detection Monitoring: Clean files after hit

I'm using LMD ("Maldet") for scanning a web server with different projects. For this purpose I'm using the inotify-monitoring. Well, the inotify-log shows, that the modified files are noticed, but I guess the filtering fails, because bad scripts are detected after running maldet -b -a /var/www/

How can I check changed files "on the fly"? I got a script in /etc/cron.daily/maldet but I do never get a daily update :-(

Thanks in advance for all your replies :-)