How to decontaminate the inner cooling system for repair, if the pumps are broken?

Hi, It is a long story, but we had some undetected biofilm in our inner cooling system of the twin tower. This seems to have blocked/broken the inner pumps. In order to have a look at the pumps and probably replace them, we would need to flush and decontaminate the system. Has anyone experience on how to do that (without the inner pumps working) ? And what solutions would be compatible with the system? Thank you for your help. It is very much appreciated.

Equipment: Sartorius Group - BIOSTAT® B