vault: Values stored securely take precedence over plain-text

Describe the bug

Assuming the following vault contents and the config file below...

{
  "/path/to/$pwd/zowe.config.json": {
    "profiles.base.properties.certFile": "old_cert.pem",
    "profiles.base.properties.certKeyFile": "old_key.pem"
  }
}

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{
    "$schema": "./zowe.schema.json",
    "profiles": {
        "zosmf": { "type": "zosmf", "properties": { "port": 443, "rejectUnauthorized": false }, "secure": [] },
        "base": {
            "type": "base",
            "properties": { "host": "my_lpar.net", "certFile": "crt.pem", "certKeyFile": "key.pem"},
            "secure": []
        }
    },
    "defaults": {
        "zosmf": "zosmf",
        "base": "base"
    },
    "autoStore": true
}

Expected and actual results

I would expect the python SDK to use the contents of the zowe.config.json as it is at the time of executing the script.

Instead, it is using the old_cert and old_key (from the vault)

Describe your environment

Py: 3.12.4
Pip: 24.0
Terminal: Zsh
Env: N/A

Additional context

Found this while testing #305

Reproduce the issue using the vault contents and zowe.config.json shown in the report, then trace how vault values are merged with the current configuration. Done means the current plain-text certFile and certKeyFile values are used instead of the older stored values; no test file or source entry point is named in the issue.