When you are stuck on real issue after doing everything nothing works like me. I also struck on similar that secondary site replication is not showing up its keep saying fail. I tried to repair but god know not working repair its getting struck on recovery state after some time its getting failed. For fixing issue below are the step taken as no important data has been store to bring up to an active state.

Issue Reported:

SCCM replication link is failed between the primary server and secondary sites.

Below are the key point and action taken to bring it up.

Step 1: We checked Database replication and found that secondary site replication failed.

Step 2: Tried recovering the secondary site from primary site however it is stuck at Recovering state.

Step 3: Steps below are to manually remove the secondary site from both the Primary site’s database as well as on the secondary site’s system as well.

On the Primary Site server:-

1. Run: %ConfigMgrProgramFilePath%\bin\X64\00000409\preinst.exe /delsite XXX *where XXX is the secondary site’s code.

2. Refresh & verify from the SCCM Console that the secondary site (and it’s system) is deleted.

On the Secondary Site server:-

Point 1: Uninstall the ConfigMgr Secondary Site from the Control Panel

Point 2: Uninstall the Microsoft SQL server and its components from the Control Panel

Point 3: Remove the secondary site’s ConfigMgr ProgramFile folder

Point 4: Remove the registry key: HKLM\Software\Microsoft\SMS

Note:- before remove registry key make sure you should take backup of registry key

Point 5: Restart the server

Step 4: Verify the prerequisites for secondary site.

Step 5: Install and configure secondary site.

Step 6: Secondary site is running as expected.

Happy Learning!!!

Thanks&regards,
Haresh Hirani
Email: [email protected], [email protected]
Facebook https://www.facebook.com/Hiraniconfigmgr-120189361980772/
Follow us: https://www.linkedin.com/in/hiraniconfigmgr 
Twitter: https://twitter.com/hiraniconfigmgr