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Consider the following scenario:
You run Microsoft Business Connectivity Services (BCS) on a server that has Microsoft SharePoint Server or Microsoft SharePoint Foundation installed.
You connect to and open a SharePoint site in Microsoft SharePoint Designer.
You create and save an external content type in SharePoint Designer.
Without closing SharePoint Designer, you switch to SharePoint Central Administration, and you grant permissions to a user for the external content type that you created.
You create an external list for the external content type on the SharePoint site.
You switch back to SharePoint Designer, change the external content type, and then you save the changes.
In this scenario, the user to whom you granted permissions for the external content type is no longer listed as a user who has permissions.
This issue occurs because SharePoint Designer saved the user permissions for the external content type when you saved it.
When you open an external content type in SharePoint Designer, the user permissions of the external content type are read. When the external content type is saved, SharePoint Designer rewrites a new external content type that overwrites all the default values, and then SharePoint Designer deletes the old external content type. This may result in any properties, localized names, and access control entries being lost.
To work around this issue, close SharePoint Designer. Then in SharePoint Central Administration, reapply the user permissions as appropriate.
Note Always make sure that you save a backup copy of the external content type before you change it in SharePoint Designer.
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.