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We have a sharepoint clone mess up, in which systems admin made a clone of sharepoint app server, but we quickly remove the newly cloned server and configured CA to other App server as it stopped working and User profile and search service also stopped working. Now CA is working on 2nd App server and I have created UPS successfully but User Profile Synchronization Service not starting and in the ULS viewer I am getting following entries:

Synchronization database was not previously initialized. Exporting the encryption key from the registry key to the database

ILM Configuration: The ExportMiisEncryptionKey process completed successfully

SetupSynchronizationService :: Sync DB failover Check :: databaseServerMiis = raqmanspdb01

SetupSynchronizationService :: Sync DB failover Check :: originalSyncConnectionString = Data Source=raqmanspdb01\mssqlspdb;Initial Catalog=UPSSyncDBNew2020;Integrated Security=True;Enlist=False;Connect Timeout=15

SetupSynchronizationService :: Sync DB failover Check:: originalSyncConnectionDataSource = raqmanspdb01\mssqlspdb

SetupSynchronizationService :: Sync DB failover Check :: new datasource string on connection object = raqmanspdb01\mssqlspdb

UserProfileApplication.SynchronizeMIIS: Begin setup for 'User Profile Service New2020'.

ILM Configuration: Configuring XML file.

ILM Configuration: Checking for existing FIM database.

ILM Configuration: Building database.

User Profile Application: Done synchronizing profile property display names for language lcid = '1033'.

ILM Configuration: Configuring certificate.

ILM Configuration: Configuring Registry keys.

ILM Configuration: Setting file permissions.

ILM Configuration: Opening firewall ports.

ILM Configuration: Starting services.

ILM Configuration: Post setup configuration.

I have checked spfarm account has permission Replicating Directory Chanes on our AD, based on above ULS log what else I should look into

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as you said you have cloned the server,one Suggestion... probably your user profile service leftover still in your new server. because Server Name (FQDN - yourServerHostName.yourdomain.com) full qualified domain name is highly depending on internal configuration on SharePoint Servers. you cannot rename or change the Domain of the SharePoint server/Farm easily because of this reason. when you clone the server all your serivice application instances will come with same name to new server. Even you rename the server.

in My opinion, you have two options

  1. One is to rebuild the server and attach to farm again as new.
  2. Second is you need to dig in to each and every detail of service application and registry to modify your server name details. but in this schenario, some services does not allow you to do the same. then you need to reconfigure the Service application again.

Some time ago I have done domain change for a SharePoint server and it was a tough activity and I have log each and every detail here change-active-directory-of-sharepoint

I think this will be helpful if you are going to explore second option.

http://www.get-spnote.com/

if you need step by step guide to configure User Profile application you can find details How to Create SharePoint 2013 User Profile Service

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