If I am understanding you correctly, you are entering in your devices into RME using the hostnames. Then, after you do an ANI Server Discovery, your RME database lists many of the devices multiple times. If this is the case, turn off "Device Synchronization" "Synchronize to Essentials". As you are already importing the devices in RME manually, there is no reason to use the Device Synchronization.
Also, you should check the SNMP community strings you are using in the discovery. The unconnected devices are probably due to a mismatched community string.