This has stepped well beyond Perl.

Unless you were using SFTP, FTP-SSL, or scp and were using a flawed OpenSSL library then this was not a Heartbleed issue. If you were then it still may not be a Heartbleed issue. If someone overwrote your FTP log files the most likely reason is to hide FTP activity.

Change your FTP passwords, and clean all the systems that ever had FTP access to the site in question as well as any on the same LAN.