I was about to post a bug report for a failed synchronization of my new phone (Nexus 5X) in MusicBee, but I managed to find a workaround. I thought my experience may be useful to anyone troubleshooting the same issues.
Here's what happened when I connected my phone - MusicBee could only identify the device as "portable device" which is not its actual name as it appears in Windows Explorer. When I proceeded to hit the synchronize button, I received this error message and was unable to continue: "Portable Device/Internal Storage" nolonger exists, you might need to change the path in device preferences." As it turns out there was no option to change the path in MusicBee, so I tried to manually fix it outside of MusicBee. First I renamed my phone in Windows (it runs in MTP mode), and then I deleted the device profile entry contained in MusicBee3Settings.ini and saved it. Now when I re-opened MusicBee my phone was automatically renamed with the proper device name "Nexus 5X" instead of "portable device", and the correct storage path was detected under the synchronization settings - resulting in a successful synchronization.