Take a look at CompleteFTPService.exe.config in the install directory.
This is basically a log4net configuration file, and you can change the location of log files there. Make a copy first!
Try modifying
%folder{CommonApplicationData}\\Enterprise Distributed Technologies\\Complete FTP\\logs\\ServiceRecent.log
to set your desired location, e.g.
D:\\CompleteFTP\\logs\\ServiceRecent.log
Of course you\'ll need to restart the service to reread the configuration file.