Yes, opened a case with NetApp and they figured it out.
The SQL connection string is stored in a xml file and in a config file. The XML was ok, but the config file (OC.Cluster.OM.Library.dll.config) was pointing to the localhost. The NetApp Support managed to generate a new config file with the correct connection string, pointing to the sql server and not for the localhost (the SCOM server). This cannot be done in notepad because as you can notice, the data needed to be changed is ciphered.
Please contact NetApp and I'm sure they will help you out.