Hi Shane,
Thanks for the information. We will aim to address this in a future release but our develop and test remains on the LTS version.
As of now, I think the best option is to pre-program your LPC-Link2 with debug probe firmware (rather than booting on demand) - so it will always appear as ID 1fc9:0090 NXP Semiconductors when connected.
We have a tool to do this called LPCScrypt LPCScrypt v1.8.0|NXP that can automate the process ... now some weasel words. This tool is pending an update to support the latest debug probe firmware etc. Although the older firmware will work without issue, you could patch an LPCScrypt installation with the latest firmware from the MCUXpresso IDE Install at ide/bin -> LPC432_CMSIS_DAP_V5_182.bin.hdr to LPCScrypt/probe_firmware_LPCLink2 . Also, the host software for this tool is 32 bit and not tested in Ubuntu 17.04.
If you have access to more than one LPC-Link2 (or another LinkServer compatible debug probe), you could perform the same programming operation using MCUXpresso IDE by connecting the debug probe to the target LPC-Link2's LPC4370 'J2' connection.
Then create a dummy project (or use any existing project), select this and click the GUI Flash Programmer 'Chip' Icon.
From the dialogue, you need to specify the flash driver as shown (else the projects driver will be used), browse to the firmware in ide/bin directory, and then set the base address of the LPC-Link2 SPIFI flash at 0x14000000, then click OK.

To use your programmed LPC-Link2 debug probe, ensure that the link JP1 (nearest the USB connector) is made and reboot the probe.
Thank you for your report and help with this issue.
Yours,
LPCXpresso Support