For some reason one of the 6509's in the network (which is in the DCR with correct credentials) is being removed from the topology map. I think I found the problem in the ani.log but don't know how to solve it. The ANI seems to conclude that these devices are the same. But they are not.
Discovery ani DcrToCampusMap: The Device container(Device,126.96.36.199 hostname: rtr-abc00m1-01.cisco.com) is duplicate of container(Device,188.8.131.52 hostname: rtr-abc00m1-02.cisco.com) , so deleting the Device 184.108.40.206 from SMFContainer