Resolution:
The EMS Manager manages connections to EMS servers in one of two ways:

Automatic discovery using HAWK or directly adding the servers to servers.xml file.

In order to undo the automatic discovery with Hawk and Routes and directly read the servers.xml file do this:

In the Builder's Tools-> Options-&gtTIBCO EMS Administration

You must uncheck the "Discover Servers using HAWK" and "Routes” check box. If you do that, no automatic discovery of EMS Servers occurs.

Now if you "Remove all Servers” and "Apply and Save Servers file” it will stick.

Once you stop looking for EMS Servers with auto Discovery, using HAWK or Routes, you must add servers to the servers.xml file, for the Builder to find them and monitor them.

The builder will read the servers.xml file on startup. Edit it to include only the servers of interest and only those will be displayed.

Note: the Builder will reflect files that Servers that are removed if auto discovery is unchecked and "Apply and Save Servers file" is done.

From the documentation:

Servers File Name

Enter the name of the file (including path, if necessary) that the EMS Manager will read to determine which servers to monitor. Default file name is servers.xml, located in the directory where you started Enterprise RTView.

NOTE: The Servers File is created when you click Apply and Save Servers File on the TIBCO EMS Servers tab. To only monitor those servers specified in the Servers File, and disable automatic discovery, deselect both Discover Servers checkboxes.

RTView EMS Manager: How does EMS manager manages connections?