How to get apfs.efi file onto the EFI partition of a drive when I can't boot the drive?

I had a brand new working and stable install of High Sierra on my SSD. I had literally just finished copying all of my files over from backup, and reinstalling all my software (Adobe suite, etc.).

Long story short, I accidentally tried booting from a drive that was not bootable. As soon as that happened, Clover stopped recognizing my SSD boot drive. My BIOS can see it, Disk Utility when run from my install USB can see it, even my Win7 install can see the High Sierra drive, but not Clover.

My best guess is somehow the apfs.efi files on the EFI portion of the drive were corrupted. I can't figure out how to add them back where they need to be. I can see the drive in multiple locations, but can't write to it from anywhere, largely because it's formatted APFS.

Is there some way to write a file to the drive using Terminal or something?