A Vault configuration is not kept the same as part of a Vault refresh on the back end.
The configuration is set to default as part of a vault refresh on the back end.
A Vault refresh sets the configuration to its default values. The Vault is placed in the same state as the source Vault from which the affected Vault is refreshed.
The proper way to maintain the current configuration in a new Vault is to have it cloned from a Production Vault. This way the configuration in the new Vault is in sync with the configuration in the Production Vault.
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