Deleting Alerted Relationships can cause sync issues unless you are not going to recreate the same relationship or the account has been decommissioned and sync is no longer required or sometimes possible. This means either the source or destination side of the relationship is not available anymore
Follow this link to actually run the tools and fix these issues:
If you have one relationship in alert, the system had a failure to log on to either or both of the source or destination folders. It could be temporary and another sync will allow it to automatically log in. But it may be because someone deleted a folder, migrated a mailbox or is hidden from the GAL. Of course, deleting the mailbox does it every time and for that you can delete the relationship and read the warnings message, then do it. Then select empty trash from the Global options and close the Add2Exchange Console, start the Add2Exchange Service and let run a full sync. If you want that relationship in alert to be active, you must fix the relationship instead of deleting it and recreating it. If you do, you will create duplication, from when the system WAS able to find the folders, with the older relationship and the new relationship and will put the same items back in. So fix it if you can! We hone in on the ids or stores of exchange servers or and something has changed. Before you delete an alerted relationship, if the mailboxes are available or moved, as in the case of an Exchange Migration or mailbox move to a different store, it is best to try to fix the relationship prior to deleting it with the Add2Exchange Recovery and Migration Manager Tool. Buy Now
If you have already deleted an alerted relationship, and want to "clean it up" of the copies, you use the Add2Exchange ToolKit to clean out the folder off all the A2E "tagged as copies" items using the Inspector General/Surgeon General option. These tools are free as part of the Value Bundle offering, or you can purchase these tools and support online separately, or in a value bundle as well.
Add2Exchange Recovery & Migration Manager (RMM)
with 4 hour block of Premier Support for $525 (sold separately $799) Buy Now
Add2Exchange ToolKit with
4 hour block of Premier Support for $525 (sold separately $799) Buy Now
Add2Exchange Move/Migration Bundle with 4 hours of Premier Support: Buy Now
Includes discounted Add2Exchange Recovery & Migration Manager Tool license,
discounted Add2Exchange ToolKit Add On Tool license,and discounted
4 hour Premium Support for $595 (sold separately $1049).
This option includes one free license transfer to the
new replacement system (value $150).
Excerpt from a Common Chat conversation
It looks as though Joel's mailbox may have been moved to a new server. Yes, this will break the relationship, sending it into alert, but is easy to repair. Use the RMM tool. If you already deleted it, use the A2E Toolsbox to clean them up and avoid causing potential duplication issues if you remake or are planning to remake the same relationship. We offer a tool called the RMM or Recovery and Migration Manager tool to fix alerted relationships.
The Toolkit is used to clean up after. Both useful Incidentally, the tools are over ½ off when on Premium Support. It is almost never a good idea to delete an alerted relationship because if you do delete an alerted relationship and then recreate it, the old relationship will still have copies there and the new relationship will cause duplication. This also will happen from an Exchange Migration. Many people think you can just reinstall it and make new relationships, and all is well, but they don't realize that the copies the old sync server made are still in the exchange mailbox they just migrated.
If you are going to remake the relationship, don't delete an alerted relationships. If the employee was terminated and you deleted the mailbox already, it doesnt matter anyway, force delete the relationships, and go to Global Options and turn on the Empty trash option, and read the screen, So either way, if no duplication is desired, or it was a poorly planned or emergency migration, and depending on what you have done prior to this chat, one of the two tools will work for you to either fix the alerted relationship before you delete them RMM or Fix them after with the Surgeon Gen.
In the future, if you want to move a mailbox, stop the Add2Exchange Service, move the mailboxes, turn the sync back on, the relationship will go into alert and then run the RMM mailbox.
Obviously you could delete the relationship and select to remove the copies then move the mailbox, then recreate the relationship, but that would be plain silly.