The problem, programming USB port disappearing problem, is NOT hardware problem but software based problem. ( In other words, If you've made a program on Atmel Studio, you can pass through all problem.) When I see the setting of Arduino M0 (Arduino.org product), which is similar configuration with ULTRA Zero series has a fuse setting as,

We should see the value of "NVMCTRL_BOOTPROT = 0x01" which is apparently different from ULTRA (ULTIMA) setting of 0x07. But this value is suitable one for "Arduino M0" bootloader and if we switch bootloader from .cc version to .org version, "0x01" is suitable but just switching value from "0x07" to "0x01" will disable binary upload mode from USB interface (USB port appears but Arduino IDE (specifically gcc) unable to upload binary).

At this moment, the proper value seems to be "0x02", as follows:

This value can be accessed and modified through Atmel Studio as shown in my previous report. Please try the following procedure, if USB port does not appear at all.

(1) Re-burning Arduino bootloader by Arduino IDE by Atmel ICE

(2) Access fuse-bit of SAMD21G18A through Atmel ICE by Atmel Studio

(3) Check and set NVMCTRL_BOOTPROT = 0x02