[Bug]: User configuration data overrides persist after user config file is removed or relocated.

[jglogan]

I have done the following

• I have searched the existing issues
• If possible, I've reproduced the issue using the 'main' branch of this project

Steps to reproduce

container system stop
mkdir -p ~/.config/container
cat > ~/.config/container/runtime-config.toml <<EOT
[dns]

domain = "test"
EOT
container system start
container system property ls
container system stop
rm ~/.config/container/runtime-config.toml
container system start
container system property ls

Problem description

Expected:

• dns.domain is present in first property listing
• dns.domain is absent in second property listing

Actual:

• dns.domain is present in first property listing
• dns.domain is present in second property listing

Environment

- OS: 26
- Xcode: 26
- Container: main

Code of Conduct

• I agree to follow this project's Code of Conduct