Before you delete a directory replication connection between one or more Microsoft Exchange Server sites, consider whether or not to run the DS/IS consistency adjuster, which compares the directory with the information store.
Warning
If you delete a directory replication connector between two sites and you plan to reconnect the two sites later, do not run the DS/IS consistency adjuster. This could result in a loss of data.
When you disconnect a directory replication connector and then run the DS/IS consistency adjuster tool, you not only prevent replication between the two sites, you also reestablish the home folder between the public folder replicas. Although all public folders that were available before you removed the connector will still be available, they cease to be exact replicas of each other. For example, if a user makes a change to a message in a public folder in Site 1 and another user changes the same message in Site 2, their changes do not appear outside the respective sites.
In addition, when the directory replication connector is removed, Microsoft Exchange Server reestablishes the home folder based on the folder where the most recent change was made. For example, if there is a public folder in Site 2 and a user edits a message in that public folder before the sites are disconnected, then the public folder in Site 2 becomes the home folder. So if the two sites are disconnected and you delete a public folder in Site 1, reconnecting causes the information store to backfill the deleted public folder to the home server (Site 2). The backfill deletes the public folder in Site 2, even if additional changes were made to it when the sites were disconnected.