More information is required to be able to give you a specific solution, but here are a few suggestions:
You can force the output of any command (even in crontab) to "disappear" with:
/path/to/some_command > /dev/null 2>&1
To clear a file, try:
cp /dev/null /path/to/some_file
or
mv /path/to/some_file /path/to/some_file_<date/time>
(then when more is written to the file, a new version is created)
I hope that helps.
Mike