update_variables_to_config loses data

update_variables_to_config loses data when called on an existing config
with numeric keys. One such example is system.site -> page.403

Even if a completely unrelated key is updated with update_variables_to_config
the value of page.403 is lost. The reason for this is that update_variables_to_config
merges the default values with the stored ones and PHP renumbers any
numeric keys starting from 0.

I will attach a test that demonstrates the issue.