[AT&T HTC One (M7)] FreeK200:
Here's the life story of my phone as far as tampering with the system files.

HTC Dev Unlock to get an unlocked bootloader

Flashed TWRP to my recovery partition

Made a backup, but I think I just included the default partitions and no more no less.

Flashed SuperSU

Used Rumrunner S-Off for AT&T 3.17.502.3 successfully

In preparation for AR31, I attempted to flash the 3.63.X.X firmware.zip, and failed miserably. One person later pointed out that it was because I was using the wrong model. Here's the log:

C:\adb>adb reboot bootloader

C:\adb>fastboot getvar all
(bootloader) version: 0.5
(bootloader) version-bootloader: 1.55.0000
(bootloader) version-baseband: 4T.20.3218.13
(bootloader) version-cpld: None
(bootloader) version-microp: None
(bootloader) version-main: 3.17.502.3
(bootloader) version-misc: PVT SHIP S-OFF
(bootloader) serialno: REMOVED
(bootloader) imei: REMOVED
(bootloader) meid: 00000000000000
(bootloader) product: m7_ul
(bootloader) platform: HBOOT-8064
(bootloader) modelid: PN0712000
(bootloader) cidnum: CWS__001
(bootloader) battery-status: good
(bootloader) battery-voltage: 4230mV
(bootloader) partition-layout: Generic
(bootloader) security: off
(bootloader) build-mode: SHIP
(bootloader) boot-mode: FASTBOOT
(bootloader) commitno-bootloader: dirty-2da61e5e88
(bootloader) hbootpreupdate: 11
(bootloader) gencheckpt: 0
all: Done!
finished. total time: 0.075s

C:\adb>fastboot reboot-bootloader
rebooting into bootloader...
OKAY [ 0.042s]
finished. total time: 0.042s

C:\adb>fastboot oem rebootRUU
...
(bootloader) Start Verify: 0
OKAY [ 0.048s]
finished. total time: 0.050s

C:\adb>fastboot flash zip C:\adb\firmware.zip
sending 'zip' (28043 KB)...
OKAY [ 2.497s]
writing 'zip'...
(bootloader) zip header checking...
(bootloader) zip info parsing...
(bootloader) checking model ID...
FAILED (remote: 41 model id check fail)
finished. total time: 2.915s

C:\adb>fastboot flash zip C:\adb\firmware.zip
sending 'zip' (28043 KB)...
OKAY [ 2.520s]
writing 'zip'...
(bootloader) zip header checking...
(bootloader) zip info parsing...
(bootloader) checking model ID...
FAILED (remote: 41 model id check fail)
finished. total time: 2.941s

C:\adb>fastboot reboot-bootloader
rebooting into bootloader...
OKAY [ 0.040s]
finished. total time: 0.040s

C:\adb>fastboot getvar all
(bootloader) version: 0.5
(bootloader) version-bootloader: 1.55.0000
(bootloader) version-baseband: 4T.20.3218.13
(bootloader) version-cpld: None
(bootloader) version-microp: None
(bootloader) version-main: 3.17.502.3
(bootloader) version-misc: PVT SHIP S-OFF
(bootloader) serialno: REMOVED
(bootloader) imei: REMOVED
(bootloader) meid: 00000000000000
(bootloader) product: m7_ul
(bootloader) platform: HBOOT-8064
(bootloader) modelid: PN0712000
(bootloader) cidnum: CWS__001
(bootloader) battery-status: good
(bootloader) battery-voltage: 4234mV
(bootloader) partition-layout: Generic
(bootloader) security: off
(bootloader) build-mode: SHIP
(bootloader) boot-mode: FASTBOOT
(bootloader) commitno-bootloader: dirty-2da61e5e88
(bootloader) hbootpreupdate: 11
(bootloader) gencheckpt: 0
all: Done!
finished. total time: 0.090s

C:\adb>fastboot oem writecid 11111111
...
(bootloader) Start Verify: 0
(bootloader) Input CID is super CID
(bootloader) Start Verify: 0
OKAY [ 0.082s]
finished. total time: 0.082s

C:\adb>fastboot reboot-bootloader
rebooting into bootloader...
OKAY [ 0.040s]
finished. total time: 0.041s

C:\adb>fastboot getvar all
(bootloader) version: 0.5
(bootloader) version-bootloader: 1.55.0000
(bootloader) version-baseband: 4T.20.3218.13
(bootloader) version-cpld: None
(bootloader) version-microp: None
(bootloader) version-main: 3.17.502.3
(bootloader) version-misc: PVT SHIP S-OFF
(bootloader) serialno: REMOVED
(bootloader) imei: REMOVED
(bootloader) meid: 00000000000000
(bootloader) product: m7_ul
(bootloader) platform: HBOOT-8064
(bootloader) modelid: PN0712000
(bootloader) cidnum: 11111111
(bootloader) battery-status: good
(bootloader) battery-voltage: 4242mV
(bootloader) partition-layout: Generic
(bootloader) security: off
(bootloader) build-mode: SHIP
(bootloader) boot-mode: FASTBOOT
(bootloader) commitno-bootloader: dirty-2da61e5e88
(bootloader) hbootpreupdate: 11
(bootloader) gencheckpt: 0
all: Done!
finished. total time: 0.084s

C:\adb>fastboot reboot-bootloader
rebooting into bootloader...
OKAY [ 0.041s]
finished. total time: 0.042s

C:\adb>fastboot flash zip C:\adb\firmware.zip
sending 'zip' (28043 KB)...
OKAY [ 2.505s]
writing 'zip'...
FAILED (remote: not allowed)
finished. total time: 2.540s

C:\adb>fastboot reboot
rebooting...

finished. total time: 0.040s

After that failed, I decided I was just going to forget about it (as it was optional and I didn't want to risk anything worse than an error message), and instead, install Android Revolution by itself instead. As I entered my bootloader, I was greeted by *TAMPERED* / *LOCKED*. The bootloader was still S-OFF, so I assumed I could install AR31 regardless. It worked, but as I'm preparing to flash the proper firmware.zip from http://xdaforums.com/showthread.php?t=2485651, it is a bit worrying to me. I already tried fastboot flash Unlock_code.bin so that I could just unlock the bootloader again and restore from the previous backup, but it refused to do so and gave me an error.

Anyways, with the information out there, should I even be worried about this considering I have S-Off? In either case, how do I solve the situation? It's a little worrying to me.