How to overwrite csv file of MySQL result set?
According to the MySQL Documentation on SELECT ... INTO


  The SELECT ... INTO OUTFILE 'file_name' form of SELECT writes the selected rows to a file. The file is created on the server host, so you must have the FILE privilege to use this syntax. file_name cannot be an existing file, which among other things prevents files such as /etc/passwd and database tables from being destroyed. The character_set_filesystem system variable controls the interpretation of the file name.


I suppose the easiest way would be the following:

STEP #1

Change this line in the query

INTO OUTFILE '/var/www/backup/AppandFllups.csv'


to this

INTO OUTFILE '/var/www/backup/AppandFllups.tmp'


STEP #2

Add these lines to the cronjob just after the dump

cd /var/www/backup
mv AppandFllups.tmp AppandFllups.csv


The main idea is to have /var/www/backup/AppandFllups.tmp be nonexistent just before the dump. The output file gets renamed to something you already use elsewhere. So, there is no need to change other processes or scripts.

Give it a Try !!!