Hi @hsdredgun!
I’m sorry but it’s not really clear what your problem is and what steps you took to address it 
Here’s how I interpreted your post, correct me if I’m wrong:
your dual-boot set up consisted in Windows, running on your HDD/SSD and Manjaro running on a USB drive.
First question, did you install Manjaro on the USB device or did you create a USB drive with persistent storage?
Or maybe you just booted with the live ISO?
Reading your second post it seems like you installed Manjaro on your nvme ssd so I don’t get the USB part
Then, you wrote:
but you don’t explain what actually happened: what are the steps, modifications or problems that led you to loose you bootloader?
Sometimes it’s just as easy as going into the BIOS, find the boot order section and select the Manjaro entry as the first boot option.
Finally,
I assume you booted in the live ISO and tried to chroot into your existing installation to reinstall GRUB.
I had to reinstall GRUB a couple of times and followed this guide on the forum, it was very helpful!
It teaches you how to manually chroot into your existing installation, so you can recover your bootloader, reinstall GRUB and so on…