Unless the user is no longer available, it is not  always a good idea to just delete an alerted relationship, because the destination side will still contain copied items and recreating that relationship may cause duplication.

If you ran a complete sync, and the deleted relationship did not clean up, it is because something is wrong with the relationship and it is in alert status. 

Usually if you delete a NON ALERTED relationship, you should to a full A2E sync and (usually) let it purge the items from the destination side of the relationship and if successful, it will automatically purge the relationship.

If the relationship is in alert, it can not purge the relationships unless you Select Empty Trash from the Add2Exchange Console and close the Console and start the Add2Exchange service.  Wait for a complete sync and do not open the Console in the middle, or you will have to reselect the Empty Trash again.

The alerted relationship is one where Add2Exchange cannot verify either the account or the source or destination folder locations. This can be caused because the account has been hidden from the GAL, the folder has been deleted or perhaps the account default email has changed because of a marriage or domain change. 

Relationships can also go into alert because of an expiration of trial of that kind of relationship or upgrading past the software assurance period.  A license would have to be applied.

Normally, you don’t want to delete an alerted relationship, because it will leave copies in the destination if it is a destination, or create orphan copies in the destination if it is a source folder.  Normally you would want to fix it if it is a default folder to avoid having to clean up.  Sometimes the relationship can come out of alert simply by unhiding it from the gal, or it can be done by moving the source or destination deleted folder from the deleted items of that user to the original location, and running the Recovery and Migration Manager tool.

If the destination folder is unavailable, you could recreate it with RMM but be careful, since if that is a source folder, recreating an empty source folder will remove the destination items of this or another relationship.

So to fix this, usually we update both the Recovery and Migration Manager tool as well as Add2Exchange Enterprise at the same time, to take advantage of the improvements, make sure in the console you have valid software assurance to do this free.

Add2Exchange Upgrade Procedures

Once the programs are installed, make sure the accounts are not hidden from the GAL and the folders are not in the deleted items container, and run the Recovery and Migration Manager.

If you delete an unalerted relationship, you are required to run a full A2E sync and (usually) let it purge the items.  If the relationship was not in alert A2E will do what you told it to do when you deleted the relationship, which was either delete the copies (usually – especially if you are going to remake the relationship),  leave them there as copies, (rarely)  or leave them there as originals (even more rare).  The deletion is automatic as long as A2E can verify the deleted relationship as correct and working.  If A2E does not verify this, as in the case if the account has been deleted or disabled, or the folder is no longer available, or the account was migrated to a new place or exchange server, this makes it temporarily unavailable to verify and will not automatically delete. 

 In a case of an alerted relationship, where A2E cannot verify the relationship source or destination, you have a decision to make.  If you know you don’t need the data cleaned up, you can select to “force delete”  by selecting Empty the trash, located Under tools, Empty Trash.  This manual intervention is for your benefit, so it does not delete a relationship which when recreating it will cause duplication.  Since the folder has to be available for A2E to “clean up”, it is that moment where we give you the opportunity to activate the account, or in the case of an alerted relationship due to a migration, you can license and run the handy Add2Exchange Recovery and Migration Manager tool to repoint and fix the relationship. 

Then, there will be no need to deleted the relationship because it is fixed.  Again if deleting an alerted relationship and then recreating the exact relationship without running the DRMM tool to fix the older one can cause duplication.  If this has happened to you, manually clean up the add2Exchange copied items in the destination folder or use the Toolkit to remove items.  Be careful when using this tool because if the folder you run it on has other relationships to it, it may cause a ripple effect and remove date unnecessarily.   This clean up can be relatively easy to accomplish if the folder is a non default folder, and the destination of a one way relationship, but harder if the destination of another relationship or the source of another relationship. 

If possible, it is almost always better to run the RMM tool to fix the alerted relationships.