[HTC One E8] Xavieritto:
You are correct about the SuperSU having blocked your update. That line certainly helped me as I was in kind of the same position as you. My device is an E8 (M8Sw) rooted, UNLOCKED and S-OFF with a supercid (11111111) and SuperSU installed. I used Sunshine to S-Off (google Sunshine S-OFF).

I was on 2.33.401.3 and I received the 2.33.401.6 update available notification. I merrily downloaded the update and went to apply. The phone booted into recovery and TWRP loaded. We can't use TWRP to install this update. We need the stock recovery. Instead of searching all around in obscure posts to find the right stock recovery, I performed these steps which ensured I had a stock recovery that would work:

Download and Install WinRAR

Boot phone as normal and connected to PC

Copied the OTA zip from the phone to the pc

Open the copied zip using WinRAR

extracted recovery.img from the zip

used htcfastboot to flash the recovery.img (htcfastboot found in an obscure post on xda. normal fastboot would probably work just as fine)

So now I thought I was good to go, and so I went. Used adb to boot to the bootloader. Selected hboot (since i still had the phone connected to the pc) and then selected recovery. Ureka! Stock recovery loaded. I selected the option to install zip from sdcard, located the zip, and then let it run, which it did. I saw a message about it not being able to unmount /data because it was in use but then it said the script was successful, result /system. Then a message saying reboot to flash firmware.zip. I was excited. I rebooted, the firmware flash. The phone rebooted gloriously with the HTC chime and then stayed at the screen with the HTC One Logo. I waited. After hours I finally gave up and did some things to the phone that I probably shouldn't have at the risk of bricking (hence I will not post what I did less anyone tries the same and blames me).

I however, had a backup. So I flashed the TWRP recovery, restored the backup, and started searching to see if anyone had my problem. I hazarded upon your post. Being the techie that I am (and the fact that i really want to get this update to work) I decided to try it without SuperSU. So I opened SuperSU, found the option to unroot phone permanently (it says permanently... i think its not), and ran it. The app closed. I rebooted the phone and when it came back up, SuperSU was gone. Ok... The upgrade process deletes the OTA zip from the phone so it was a good thing I had it copied. I copied it from the PC to the phone SD. Since I had TWRP reinstalled, I once again flashed the stock recovery. And off I went again. All went as before up to the "reboot to flash firmware".

I rebooted and took note of the time. 6:55 pm. The phone rebooted, firmware flashed, glorious HTC chime once again. Then the logo screen.

One minute passed. I said OK, I will give it 10. To my surprise it went to another screen! "Android is upgrading" and the apps counting (up to 249). HOORAY!!

20 mins passed and the phone was up and running. I got the message that the update to 2.33.401.6 was successful.

So SuperSU had to go.

I read some posts that stated:

supercid's block the installs

Need to be S-ON

Need to be LOCKED

I did this with supercid (11111111), S-OFF and UNLOCKED.

Unfortunately my backups are not clean. I took them after adding my accounts so I cannot post.

My getvar:

(bootloader) version: 0.5

(bootloader) version-bootloader: 3.19.0.0000

(bootloader) version-baseband: 1.24.30306251.15G

(bootloader) version-cpld: None

(bootloader) version-microp: None

(bootloader) version-main: 2.33.401.6

(bootloader) version-misc: PVT SHIP S-OFF

(bootloader) serialno: -=REMOVED=-

(bootloader) imei: -=REMOVED=-

(bootloader) imei2: -=REMOVED=-

(bootloader) meid: -=REMOVED=-

(bootloader) product: mec_dugl

(bootloader) platform: hTCBmsm8974

(bootloader) modelid: 0PAJ21000

(bootloader) cidnum: 11111111

(bootloader) battery-status: good

(bootloader) battery-voltage: 0mV

(bootloader) partition-layout: Generic

(bootloader) security: off

(bootloader) build-mode: SHIP

(bootloader) boot-mode: FASTBOOT

(bootloader) commitno-bootloader: 106a5266

(bootloader) hbootpreupdate: 11

(bootloader) gencheckpt: 0

all: Done!

finished. total time: 0.026s