HDD (windows HDD + bootloader)
USB Stick (live installer): 16GB stick Flashed with Manjaro ISO (using this for installation)
USB Stick 2 (main): 32GB flash drive where I want to install manjaro.
Right now, I have installed manjaro on the 32GB flash drive and configured it to my taste. But the problem is that the bootloader is installed on the Windows drive (replaced windows default bootloader).
Now whenever I disconnect and reconnect my USB stick, it just throws grub into rescue mode since it cant detect the USB properly.
What I want to do:
Shift grub to the USB drive, and resurrect my old windows boot loader
Or reformat the whole 32GB USB stick with 3 partitions (boot loader + swap + Manjaro) while keeping all my data and configs from the previous manjaro install.
If it is replaced, then i assume you mean not a UEFI, but a BIOS setup.
You will have to repair the windows bootloader.
Since grub is installed on the flash drive, you will have to write the MBR (Master Boot Record) on that drive and not on the windows HDD. You will need to boot a live session, chroot into the flash drive and reinstall grub there again: GRUB/Restore the GRUB Bootloader - Manjaro