This is what I've tried... but for some reason "model("user").primaryKey() is still returning the old "User_Id" column...
<cfset table("user_table")>
<cfset property(name="id", column="User_Id") />
<cfset setPrimaryKey(property="id") />
UPDATE
The problem lies within the "Scaffold" plugin.
It's using the "COLUMNLIST" instead of the "PROPERTYLIST"
I've repaired this and it seems to be generating properly now.