Difficult one. If this is a new installation I'd suggest you roll back the whole installations and start over. 

If this is not an option I'd suggest you contact Nintex support and check if they can help you. Maybe you can use Nintex' PowerShell component to remap the configuration database but never did this on my own. 

Best regards

Enrico

We did open a ticket. Apparently, this should do the trick

$farm = Get-SPFarm;

$farm.properties["NW2007ConfigurationDatabase"];

$farm.properties["NW2007ConfigurationDatabase"] = “”; $farm.Update();

...unfortunately, we found other documentation on uninstalling the products, which indicated that

$farm.properties.Remove("NW2007ConfigurationDatabase") would clear the instance. It did, but now we cannot get the NintexWorkflow2016 feature to deploy.

Fools rush in, where angels fear to tread.

I think that only Nintex support can help you with this one. However, once they solved the ticket with you it would surely be helpful for others to post what the final solution to this problem was.

Hope you get that problem fixed quick.

Best regards

Enrico