We've been experiencing a large number of resource merges and have determined that network discovery and agent managed machines aren't entirely compatible. The tool was brought in to discover resources and manage them. The discovery would need to be run periodically to pick up new items. Now a problem occurs when a machine is renamed. The keys created in the ResourceKey table by Network Discovery are not updated during a rename. If the name gets reused, there will be a merge.
Support has kindly provided a script to remove these keys via an SQL trigger. They have also stated that reusing computer names is not a good practice; I believe there is a howto on this topic.
What other keys does Network Discovery create that may not be updated? We are using ICMP, SNMP, and WMI. The latest discovery I ran against a machine created: macaddress, host.uuid, and hostname. It also slightly changed the name.domain key. On other machines I've seen it create nbname.domain. I'm guessing none of these keys created by network discovery would get updated; therefore, all off them would need to be removed to prevent merging on keys outdated keys.