Okay thats good, I've done exactly that. So the bootloader you've created is for the Arduino Zero Native Port, I know this is sounding picky, but is there anyway to change it so the bootloader is for the Arduino MKRZERO instead? If its too much to ask then I'll make do.
So I don't think the USB part is working. I've had the EDBG Chip connected the entire time and when you turn that off, COM 6 disappears even though I still have a USB connected directly to the SAMD21G15B Chip?
I believe you just need to change the BOARD_ID on line 60 in the Makefile from "arduino_zero" to "arduino_mkrzero", this should then switch the boards definition file over to the MKR Zero's.
Once the bootloader's uploaded, you should be able to remove the programmer and upload from the Arduino IDE over the microcontroller's native USB port.
Yeah that bit doesn't work, it doesn't like it when you remove the programmer. Even though you select COM 6 on the port when uploading sketches it seems as though it uploads through the programmer still
I uploaded the modified bootloader and used the replacement bossac.exe, together with Arduino SAMD core setup for 32KB flash and 4KB RAM on my SAMD21G18A custom board.
It all functioned successfully, so it should work OK.
I'll install the SAMD Package again on Arduino IDE, then go through the steps again. I'll let you know how I get on tomorrow. Should I try a brand new chip and see if that works as well?