I suggest opening a support case.
When you brought up the new controllers, did you use the same IPs as the old controllers? Do you care at all about the historical data? If so, you can navigate to the older controller entry, click to the manage tab, at the bottom there's a replace hardware button, click it and select the newer controller and then save/apply. This will combine the older historical graphed data to the newer entry.
I'm surprised that the delete didn't go through though. Can you tail /var/log/httpd/error_log and attempt to delete the controller from the UI again? If there's a crash message, then that would explain why it looks like nothing is happening and a support case would help clear that up.
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