This has become one issue after the next.
As the title implies, windows nuked my EFI partition for Manjaro, as I found out when I booted straight into windows, skipping GRUB. Checking my partitions using a LiveUSB shows that my mountpoints and flags were removed. Tring to reset the flags does nothing. My partition setup was as follows.
EFI for windows
"Microsoft reserved partition"
EFI for Manjaro (FAT32)
How can I get Manjaro to regenerate the EFI partition?