I think this needs more studying, I'm not sating it's not an issue, but I just checked mount points for each partition in adb checking the mounts folder, and that shows this:
/dev/block/mmcblk0p3 /efs ext4 rw,nosuid,nodev,noatime,barrier=1,journal_async_co mmit,data=ordered 0 0
which tells me that /efs is not seen as a folder, but a seperate partition with the mount point mmcblk0p3. Therefore unless the Odin tar has an efs.img inside it cannot be changed flashing a stock rom, and this rom only contains system, recovery, boot, modem, cache, hidden, bootloader and trustzone, so by all rights the update cannot change the efs, therefore the problem you are explaining must be down to something else.
Device: Samsung Galaxy S3.
ROM: Whatever I feel like at any one time
Kernel: Please see above