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You cannot delete a custom many-to-many relationship after you run the Microsoft.Crm.SE.FixMissingBulkDeleteFailureRelationship.exe tool in Microsoft Dynamics CRM 4.0
Article ID: 978103 - View products that this article applies to.
Consider the following scenario in Microsoft Dynamics CRM 4.0. You create a custom many-to-many relationship. Then, you run the Microsoft.Crm.SE.FixMissingBulkDeleteFailureRelationship.exe tool. In this scenario, you cannot delete the custom many-to-many relationship.
Note To obtain the Microsoft.Crm.SE.FixMissingBulkDeleteFailureRelationship.exe tool, apply the hotfix that is described in the following Microsoft Knowledge Base (KB) article:
(http://support.microsoft.com/kb/954322/ )Error message when you import some customizations to an upgraded installation of Microsoft Dynamics CRM 4.0: "Either the file could not be uploaded or Import failed"
This problem occurs because there is an error in the Microsoft.Crm.SE.FixMissingBulkDeleteFailureRelationship.exe tool.
This problem is fixed in the latest cumulative update rollup for Microsoft Dynamics CRM 4.0.
For more information, click the following article number to view the article in the Microsoft Knowledge Base:
(http://support.microsoft.com/kb/949256/ )Microsoft Dynamics CRM 4.0 updates and hotfixes
After you install the latest update rollup, you must contact Microsoft Dynamics CRM Support if you have relationships that are affected by this issue.
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.