Hello amir sherafatian,
There is a solution to your problem but you should note that this is expected behaviour. The tool that modifies the database schema is usually run on one class library, this means that the UpgradeDatabase property on the project is only set to true in one of the projects. I suspect that this is not the case in your solution, and you have this option set to true to all of your projects.
This means that when the specified project has finished building, the schema tool is run and it modifies the database schema. In order however to upgrade correctly the schema tool has to know of which assemblies the model is consisted. This happens through the app.config file. In it there is an openaccess section that has an references child node. You can find more information on this in this help article.
So what you need to do is to create this <references> section in the app.config of one of the class libraries which references the other two. Then you should set the UpgradeDatabase of the referenced projects to false and only set it to true in this class library project.
When you then build the chosen Class Library project, your database will be correctly updated.
I do hope this helps. If you need more information please contact us back.
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