Hi, looks like the culprit is a /etc/cron.daily/do-agent cron-job which executes the /opt/digitalocean/do-agent/scripts/update.sh script which includes following if statement:
if command -v apt-get 2&>/dev/null; then apt-get -qq update -o Dir::Etc::sourcelist="sources.list.d/digitalocean-agent.list" -o Dir::Etc::sourceparts="-" -o APT::Get::List-Cleanup="1" apt-get -qq install -y --only-upgrade do-agent /* output removed for brevity */ '-o APT::Get::List-Cleanup="1"' flushes other repositories.. Martin