linux - Repair Windows 10 boot loader

I am having trouble repairing my Windows 10 boot loader. I have tried booting into the Windows 10 installer usb and doing the Repair Start Up there. I have tried the solution suggested here: How to fix Windows 10 boot loader from Windows . I have also tried the fix detailed here: http://www.fixedbyvonnie.com/2013/12/how-to-repair-the-efi-bootloader-in-windows-8/ . Neither of these fixed the issue for me.

The history behind the issue is this: I initially installed Windows 8.1 onto my primary boot ssd. I later repartitioned and installed Arch Linux onto a second partition on the same drive. I then installed Windows 10 over top of the Arch Linux installation. I later removed the Windows 8.1 partition and re-expanded so that Windows 10 was the only OS installed on the drive. (I later added a second ssd with Antergos Linux on it.) This series of installations seem to have left the Arch gummiboot boot loader on the drive, though if I just booted the drive directly it always dumped me directly into the Windows boot loader, so I didn't even realise the Linux gummiboot loader was still present.

I have been trying to get a GPU passthrough setup working [https://www.reddit.com/r/pcmasterrace/comments/3lno0t/gpu_passthrough_revisited_an_updated_guide_on_how/ ] and I couldn't get Windows working in the Virtual Machine, and determined that it seemed to be because of the boot loader. I tried various methods of fixing this (as above), but nothing worked. So I looked at the ssd Windows 10 was installed on and saw that there was still a ext4 partition (alongside of a fat32 partition, which is where Windows had it UEFI boot loader). I deleted the ext4 partition and set the "boot" flag on the fat32 partition. After doing this, now not only did running Windows in a VM no longer work, but I was no longer able to boot directly into Windows. Now I get a "PROCESS1_INITIALIZATION_FAILED' error on boot.

I went into the fat32 partition and found that there was still a gummiboot directory. I tried deleting that, but it made no difference. I then deleted all files from the fat32 partition and re-tried the solutions from the first paragraph. Still nothing works. Though I now have 6 different (all non-working) Windows Bootloader entries when I go into the motherboard BIOS.

Is there any way of fixing this, aside from completely reinstalling Windows 10? And, if I have to reinstall Windows 10, is there any way to save the current partition where the actual Windows 10 installation is (as opposed to the EFI/boot partitions) and dump it over top of a new installation? (And how do I remove all of the Windows 10 bootloader entries from BIOS?)