Make sure you delete all the while spaces in the empty function, then save the file and re-load it from hard disk. It shouldn't be printed if it is completely empty. If this doesn't work on your version of TRiLOGI, then update your TriLOGI by following the "Upgrade" path in your "Help" menu.
If you want to use a text editor to edit it, make sure that you make a back up copy and work on the backup copy first.
Note that the function number are represented as zero offset in the file. So to clear CF #6, you can look for the text such as "Fn#5, nn where nn is a number. Then delete the lines from the line "Fn#5, nn" up to the next "Fn#" and the CF will be removed.