I have had this issue before, and what I had to do was log onto the node directly, and run the SolarWinds clear certs script. It essentially stops the services, deletes all the files in the spop directory, and restarts the services. Once you restart the services, the nodes pop into the SEM again. Here is an excerpt of the .bat file/script that shows all the files to be deleted, and their locations (pasted as plain text):
del \\%1\c$\windows\sysWOW64\contegospop\spop\communications.xml
del \\%1\c$\windows\sysWOW64\contegospop\spop\alertdb.xml
del \\%1\c$\windows\sysWOW64\contegospop\spop\database_cfg.xml
del \\%1\c$\windows\sysWOW64\contegospop\spop\datadictionary.xml
del \\%1\c$\windows\sysWOW64\contegospop\spop\hierarchy.trigeo
del \\%1\c$\windows\sysWOW64\contegospop\spop\peer.trigeo
del \\%1\c$\windows\sysWOW64\contegospop\spop\private.trigeo
del \\%1\c$\windows\sysWOW64\contegospop\spop\StartupRules.xml
You can run this from any machine that will have access to all the machines that you need to have in the SEM, and the account you run the .bat file will need admin rights. You can create a ticket and request the clear certs script - SW should be able to help you with it...if not let me know if I can help
Respectfully,
Mike