Introduction

I would like to share what I have understood about working with more than one Web.config file from my latest ASP.NET application. We planned to have different Web.config files for sub-folders in the application root folder. It helps us to have small and easily maintainable configuration files.

Hierarchy of Web.config Files

System wide configuration settings are defined in the Machine.config for the .NET Framework. The Machine.config file is located in the C:\WINDOWS\Microsoft.NET\Framework\v1.1.4322\CONFIG folder. The settings defined in this file are applicable to all ASP.NET applications in that system.
We can override these default settings by including a Web.config file in the application's root folder.
By including Web.config files in sub-folders, we can override the settings defined in the Web.config file in the application's root folder.
The following are sample section declarations from a Machine.config file:

<section name="processModel" 
  type="System.Web.Configuration.ProcessModelConfigurationHandler, 
        System.Web, Version=1.0.5000.0, Culture=neutral, 
        PublicKeyToken=b03f5f7f11d50a3a" 
  allowDefinition="MachineOnly"/>
 
<section name="sessionState" 
  type="System.Web.SessionState.SessionStateSectionHandler, 
        System.Web, Version=1.0.5000.0, Culture=neutral, 
        PublicKeyToken=b03f5f7f11d50a3a" 
  allowDefinition="MachineToApplication"/>
 
<section name="appSettings" 
  type="System.Configuration.NameValueFileSectionHandler, System,
        Version=1.0.5000.0, Culture=neutral, 
        PublicKeyToken=b77a5c561934e089"/>

There is an attribute allowDefinition specified in the first two section declarations with the values: MachineOnly and MachineToApplication.

What it does mean?

If allowDefinition="MachineOnly", then we can not override this section either in application level or in folder level. The only section declared in the Machine.config file with this settings is processModel.
If allowDefinition="MachineToApplication", then we can override these sections by the root directory Web.config. Sections with this setting in Machine.config are authentication, machineKey, sessionState, trust, and securityPolicy.
If allowDefinition attribute is omitted in a section declaration of the Machine.config file, we can override that section at any level.
We can override the section appSettings at any level and can access it by using ConfigurationSettings.AppSettings easily.

What is there in the sample project?

The sample source code is a simple ASP.NET web application with three Web Forms and three Web.config files. The root folder has a sub folder SubFolder_L1 that has SubFolder_L2, each has one Web Form and one Web.config file.
Web.config files have different and overridden keys. Web.config file in the root folder has the following appSettings declarations:

<appSettings>
    <add key="root" value="Root folder's configuration file."/>
    <add key="color" value="Blue"/>
</appSettings>

Web.config file in Subfolder_L1 has the following appSettings declarations:

<appSettings>
    <add key="subfolder_l1" value="Subfolder_L1\web.config file."/>
    <add key="color" value="Green"/>
</appSettings>

The color setting is overridden by the subfolder configuration file. We can read the root element from Subfolder_L1 or Subfolder_L2 by the following code:

lblConfig.Text = ConfigurationSettings.AppSettings["root"];

But we can not read configuration settings defined in Subfolder_L1's Web.config file from the root folder.

License

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Based on my understanding, you have two web.config files. One is in the root directory and another is in the sub-directory. If I have misunderstood it, please let me.
For this scenario, the root cause is some elements in web.config don't allow sub-directory level. All of those elements have an attribute: allowDefinition="MachineToApplication". It means we can only define those elements in machine level and root application level.
To solve this issue, please remove the elements (in the sub-directory web.config) which can result in this problem. For example: membership, roleManager, sessionState, authentication, and so on. They can automatically inherits from the root web.config