Spectrum will not remove a connection unless there is data to indicate a new connection should be created. We remove the connectivity only if the same port is resolved with a different port through AutoDiscovery otherwise the connection never be removed.
From the autodiscovery debug log the current existing link between UWVNLAMxxxxxx.ortus_Gi4/0/5 and UWVNLAMyyyyyy.ortus_Gi1/0/50 is not removed because both interfaces are no longer connected with any other port.
On the contrary if an interface is connected to a new interface the existing link is deleted and the new connection created... eg.
Jul 16 21:30:59 Replace Network for Port UWVNLAMxxxxxx.ortus_Gi1/0/49(ifType=6) having potential connections :1
Jul 16 21:30:59 Port UWVNLAMxxxxxx.ortus_Gi1/0/49(ifType=6) <--> Port UWVNLAMyyyyyy.ortus_Gi1/0/52(ifType=6)
Jul 16 21:30:59 creating Layer-2 connections.
Connection was removed: Port UWVNLAMxxxxxx.ortus_Gi1/0/49(ifType=6) <--> Port UWVNLAMyyyyyy.ortus_Gi3/0/5(ifType=6)
Connection created ( ( Cisco CDP): Port UWVNLAMxxxxxx.ortus_Gi1/0/49(ifType=6) <--> Port UWVNLAMyyyyyy.ortus_Gi1/0/52(ifType=6)
NOTE: CA Spectrum discovery will not always remove old/stale connections unless the connection has been updated on an interface that had a previous connection. For example, if you have a connection on Fa0 <->Fa0 and you change it to Fa1<->Fa1, Spectrum will create the new connection on Fa1<->Fa1 and will leave the old Fa0<->Fa0 connection there but If you updated the connection from Fa0<->Fa0 to Fa0<->Fa1, then Spectrum WILL destroy the connection Fa0<->Fa0 and create the Fa0<->Fa1 connection.