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SQLiteConnection.Execute is not affecting
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> <code>var parameters = new { ConfigParameter = ConfigParameter, ConfigValue = ConfigValue };
</code>

Perhaps, in the interest of clarity, you could initialize with literals to avoid extraneous questions such as "What are the values of ...?"

> var sql = ... " set  ConfigValue = '@ConfigValue' " ...

That's almost certainly not what you intend. Parameter substitution does not occur inside of SQL string literals.

> But it doesn't impact the DB.

I suppose that by "impact" you mean "alter". I have no idea whether this is because the DB already contains the values you set in this code or something else is going on.