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The problem is that whoever is creating the RPM spec files doesn’t know what they’re doing. The rpm spec is deleting it’s own files on upgrade. And for bonus points literally obsoleting itself, so executing a reinstall doesn’t work either.
The short term solution is, every time there’s an update, and it cripples itself, completely uninstall the rpm, then re-install.
I have the same error on Ubuntu 18.04, so it doesn’t look like something specific to RPM. Manual execution of
apt-get update -o Dir::Etc::sourcelist="sources.list.d/digitalocean-agent.list" -o Dir::Etc::sourceparts="-" -o APT::Get::List-Cleanup="1"
apt-get install --only-upgrade do-agent
(from update.sh script) works correctly.