Here I document how, in Eclipse, to start two, concurrent debugging sessions to two NRF5DK boards (or other debugging probes) , connected to different USB ports of the same computer.
The sessions will appear as separate items in the list of threads in the "Debug" frame of the "Debug perspective". When you select one, the other windows of the perspective show contents of, or control, the selected session.
To do this, you need two "Debug configurations", having distinct port and "USB serial" values.
You can easily clone your usual debug configuration: choose Debug>Debug Configurations. Expect a dialog to open, listing your debug configurations under "GDB SEGGER J-Link Debugging." Select your existing configuration, e.g. "Foo", then chose the "Duplicates the selected configuration" icon in the upper left. The duplicated debug configuration will have name like "Foo (1)".
The usual debugging configuration, under the "Debugger" tab, under "J-Link GDB Server Setup" banner, uses GDB, SWO, and Telnet ports: 2331, 2332, and 2333. It also has an empty "(USB serial..." text field. Leave the ports as is, but enter the serial number of one of your debug probes (NRF52DK's.)
For the cloned configuration, use ports 2400, 2401, and 2402, and the serial number of your other debugging probe.
You can find the serial numbers of your debugging probes on linux command line using "lsusb -v". The serial number is labeled "iSerial". An example serial number is 682102069.
Addendum: how to start multiple RTT clients for the SEGGER RTT log: The Segger GDBServer also serves RTT to an RTT client via a port, which defaults to 19021. You can used the defaults for your first debugging/logging sesssion. For your second session, in the Debug Configuration>Debugger> Other Options field, add "-RTTTelnetPort 19101" and when you start JLinkRTTClient (in a terminal) add the option "-RTTTelnetPort 19101".