When you program in for debugging you are writing direct to the chip, this deletes the bootloader! You'll want to restore it if you ever want to go back to using the Arduino IDE.
This is pretty easy. Launch the IDE, select Arduino Zero (programming port) from the Tools->Board menu, and Atmel EDBG as the Tools->Programmer
Then select Burn Bootloader
It only takes a few seconds to burn in the bootloader:
For this, you'll need to use the Atmel Studio setup, since you're using a J-Link.
Download the bootloader hex file
Wire it up correctly and select Device Programming
Select J-Link and the ATSMD21G18A with SWD. Verify you can read the Device Signature
Unlock the Bootloader protection by going to Fuses and changing BOOTPROT to
0x07 then programming
Next click on Memories in the left hand side
Next to the Flash (256 KB) section, click the triple-dots and select the bootloader file.
Then click Program to program it in