look in the online help of your CiscoWorks LMS server:
http://YourLmsServer:1741/help/cmf/index.html?logrot.html
and be aware of section 5. :
[..]
Only log files that reach 90% of their size limits are backed up, and the original log file is emptied.
[...]
The size limits for the log files are defined in $NMSROOT/conf/logstat.conf with values in bytes. So if a log file has not reached 90% of this predefined value OR is even not listed in this file it will not be touched be logBackup.pl (on Windows, some log files are also defined in the registry)
logBackup.pl was the first utility to handle log file size, but the daemon manger must be stopped to execute it. I would recommend to configure logrot.pl instead to handle log files and have the daemons running. See the above online help link to get details about logrot.pl and also search this forum - there are multiple threads with this issue.
If you have configured logrot.pl properly you do not need to delete log files manually.