I had a similar issue, I created a new sources.list file which held only the sources I wanted Apticron to work with
And then I changed the Apticron code so it will use the file I created.
sudo grep "-security" /etc/apt/sources.list | sudo grep -v "#" > /etc/apt/security.sources.list
Above command will create a new sources list specifically for security.
Inside the /usr/sbin/apticron code I made the following changes.
Update the package lists
/usr/bin/apt-get -qq update -o Dir::Etc::SourceList=/etc/apt/security.sources.list || true
Get the list of packages which are pending an upgrade
PKGNAMES=`/usr/bin/apt-get -o Dir::Etc::SourceList=/etc/apt/security.sources.list -q -y --ignore-hold --allow-unauthenticated -s dist-upgrade | \
/bin/grep ^Inst | /usr/bin/cut -d\ -f2 | /usr/bin/sort`
It did work for me. This link contains tutorial how to create and use a different source.list for apt-get.