As you still have your old SIM use that setup to replicate the new SIM certificate to the other Windows servers. So first use one template server and add the certificate from the new server by logging in to that servers SMH, go to settings > Security > Trusted Management Servers. Select the Get Certificate Information, type your new SIm server IP or name and add the certificate. Now you should have two certificates. With this server you can fix your other servers trust with the new SIM server.
Now select all your Windows servers exept the one we just fixed. Then go to Configure Replicate Agent Settings. At the first screen select your source server, this would be the server we just fixed. The server shows more options, the first would be Hp System Management Homepage. Click on the plus, go to Settings > Trusted Certificate Properties and select both certificates. If you also have a VCRM you can switch your repository at a later stage when you've copied your SPP's from the old SIm server to the new setup. You can now push the Run Now button. If this does not work you probably did not have a trust on the old SIM server to begin with. Once you've completed the replication you now have a trust with the new SIM server. Once this is functioning logiin to your new server run a Identify for your servers an d start with selecting your Windows servers and select Configure > Configure or Repair Agents to repair/set your SNMP and or WBEM settings.
This little manual can also be used for Unix servers. ESX server from 5.1 no longer use trusts so the whole trust thing is not needed on ESX 5.1 and above.