After changing a record's primary business relationship in the Raiser's Edge and running synchronization, the information is then deleted from Education Edge and Raiser's Edge records. The organization record exists in both databases and they are linked together. Sometimes the deletion does not occur until the second synch after the change is made.
We resolved this issue in version 7.82.104, patch 9.
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.
Alternative Solution: Make the changes from Education Edge instead of Raiser's Edge: 1. Make the current primary business no longer the primary business in Education Edge 2. Add the new primary business relationship to the record 3. Sync