Hi Robert,
we had a same issue in SAP BO 3.1 SP3. we had 14000 users and 900 Win Ad groups.
Suddenly we have lost all the Win AD groups in the Bo environment.Hence we have lost all the Users/personal documents we have lost.
Below is the issue description:
1755220 - Can LDAP or AD groups get deleted by network communcation issues with AD/LDAP?
Later we have raised SAP Incident for the same. Restoring the CMS DB was the only solution provided.
to avoid this issue in future our expert and to the Alex have suggested the same to create Enterprise alias for all the users and Create enterprise groups instead of directly applying security with the Win Ad groups.
1401058 - How to create Enterprise aliases for LDAP or AD accounts