I managed to fix it! I copied the files I could access from the EFI partition as a backup and reformatted the partition as FAT32 and readded the flags “boot” and “esp”. I then changed the UUID in /etc/fstab corresponding to the /efi partition to the newly assigned UUID.
I chrooted to /mnt after mounting both partitions as before and ran bootctl --path=/efi install" to reinstall systemd-boot. I finally ran reinstall-kernels and it added back files to the efi partition and a loader configuration. I tried restarting and I got back into my EndeavourOS installation! 
However, there was no boot menu. But I fixed this by copying over configuration from my backup (adding timeout etc). I also copied over the old directory in /etc/ETC/Microsoft since Windows 10 had disappeared from the boot partition this time, and now both are there.
For future reference, my current loader.conf file is:
default 3690eb269c5148009b215f3193003ce6*
timeout 5
console-mode auto
reboot-for-bitlocker 1