Employee and subsidiary relationships are end dated invalidly when a single subsidiary ends it's relationship with the parent organization.

When the option 'Set end date for relationships between subsidiaries and intermediate/top parents when no longer valid' is marked and a subsidiary is marked to no longer have an organization as a parent, all other subsidiaries and the parent organizations employees are end dated. 
To check current Relationship settings:
  1. As an administrator, log into CRM and click the Constituents functional area
  2. Click "Relationships settings" task
  3. Navigate to the Corprate Relationships tab
  4. Note value under "Top parent and subsidiary relationship" 
  5. If "Set end date for relationships between subsidiaries and intermediate/top parents when no longer valid" is marked: Yes
    1. Click Edit, the Configure corporate relationships window appears
    2. Uncheck "Set end dates for relationships between subsidiaries and intermediate/top parents when no longer valid
    3. Save these changes
As a precaution, check Parent organization records.  If you've been impacted by this, you will see end-dates for the same day spaning many relationships. A SQL script can be supplied to verify affected records provided RELATIONSHIPAUDIT and ORGANIZATIONDATAAUDIT audit tables are enabled.  Contact Support and reference this article. 


Download and install the latest patch, which contains all fixes from previous patches. If you are running an older version, download and install the latest version and then the patch. 

Environment

 2.9, 2,91, 2,93, 2.94, 3.0
 3.0.516, Service Pack 9 ; 2.94.1524, patch 105

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