From the updater-script(edited for brevity):
ui_print("Removing unneeded files...");
delete("/system/bin/iqmsd","/system/lib/libiq_client.so", "/system/lib/libiq_service.so")
But.....and this is a BIG but(pun intended)....it looks like everything has to be stock or the update will fail and leave a mess behind...as interdpth is unfortunately finding out now.....
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Edit: More info....the updater-script verifies files in /system but does not flash the kernel till later:
apply_patch("EMMC:/dev/block/mmcblk0p8:4468736:8ff468aad3df4901b506dc3ff6579487f5812aa6:4472832:fafa28534994de883c7d48df488cdb53a1a67224",
"-", fafa28534994de883c7d48df488cdb53a1a67224, 4472832,
8ff468aad3df4901b506dc3ff6579487f5812aa6, package_extract_file("patch/boot.img.p"));
I suppose if the /system patches are applied but that ^^^ fails, you would get a reboot into recovery so make sure you have the stock kernel flashed before you do the OTA update. I would suggest using Odin to flash back to stock recovery just to be safe but I don't know yet if that is necessary.
Edit2:
applypatch EMMC:/dev/block/mmcblk0p8:4472832:fafa28534994de883c7d48df488cdb53a1a67224 EMMC:/dev/block/mmcblk0p13 0e3e73ed806dcb0ec7f823846936ebe748968d38 4722688 fafa28534994de883c7d48df488cdb53a1a67224:/system/recovery-from-boot.p
Looks like it overwrites recovery no matter whats there.