Sounds like you are running out of USB bandwidth. It also sounds like you have programmed in very very old Link2 firmware.
Try using LPCScrypt (http://www.nxp.com/lpcscrypt) to program up both probes with the latest firmware, and make sure you program at least one of the debug probes with "non-bridged" version of the firmware. The "LPC-Link2 Debug Probe Firmware Programming Guide" supplied as part of LPCScrypt explains how to do this.
This will mean that one of your probes looses vcom port capability but should reduce the USB bandwidth requirements sufficiently to generally allowing debugging of both setups to be carried out in parallel. (Note that you may need to reboot your PC first though).
Regards,
MCUXpresso IDE Support