The problems with unusable nodes may normally occur only if model elements are not defined in the application model. For instance, you might move Web differences (one layer) to a WinForms or platform-agnostic module project (another layer with a different schema that knows nothing about Web). Or you might remove certain model elements from the application model yourself. More information on this can be found at Why application model differences can be removed into the UnusableNodes.xml file

Normally, these problems should not occur at all if you use the Model Editor and Merge Model tools and do not edit the XAFML files manually.
You can learn more about means of detecting unusable nodes at http://documentation.devexpress.com/#Xaf/CustomDocument3327

So, these are three simple steps you can follow to avoid any problems:
1. Use Model Editor and Merge Model tools to perform operations with the application model;
2. Do not edit XAFML files manually unless you are absolutely certain of what you are doing;
3. Verify that XAFML files do not contain references to removed custom model elements extensions

If this information does not help you to fix unusable nodes in your model, you are welcome to provide us with the XAFML file (or rather a small sample project) before unusable nodes appear + exact steps that cause it + the XAFML file after executing these steps. We will be glad to help you resolve this.