[HTC EVO 3D] freeza:
I was on a hunt to make this work without losing any data and I've figured out a way that works quite nice, and all it involves is a TWRP backup, ADB, and a bit of commandline.

Thanks to TrevE for his ever evolving tweaks to Android and for making them readily available to the community at the cost of one thanks per post, and maybe a beer or two (how many people really buy beer with donations?!) :D

Required:

TWRP backup

ADB

The EXT4 tweaks for /data

The EXT4 tweaks for /system

(If your ROM doesn't already have them, I will be providing the zips for them courtesy of Synergy.)

Step 1:

Connect your phone to your PC and like all things of this nature, BACKUP! Use TWRP to create a nandroid of your entire phone. We will need this backup to restore data and system via commandline. TWRP is the only tested method that works, since it creates backups that are actually TAR files (God, I love TWRP for this). Stay in recovery after completing backup.

Step 2:

While still in recovery, enable USB storage mode and download the two EXT4 files below (or applicable if your ROM already has one of the partitions optimized) onto the root of your microSD card. To make things easier, you can temporarily move your data.win and system.win files to the root of your microSD card. They are located in the TWRP folder on your microSD card. Afterward, disable USB storage mode.

Next, there are TWO ways to accomplish this. Choose which way you want to go before continuing.

Method 1: Reflash your ROM(NOT RIGHT NOW, later on in the guide--depending on ROM, this may format your /system and/or data partitions, rendering the tweaks useless.)

Method 2: Use commandline to restore your ROM from TWRP backup.

Step 3:

From recovery, wipe dalvik and cache and format data and and depending on method, your system partitions as well. NOTE: formatting the partitions can be done from TWRP in the advanced menu.

Step 4:

Flash the applicable EXT4 file.

Step 5:

Mount /data, /system, (if applicable), and /sdcard with TWRP and launch an ADB shell by typing "adb shell" then press enter while in your ADB folder from command prompt/terminal.

Step 6:

Type "cd /sdcard" and press enter. To make sure you're in your sdcard, type "ls" then press enter to verify that it's listing your microSD card contents.

Step 7:

Type "cd /data" and press enter. To make sure you're in /data, type "ls" then press enter to verify that it's empty. It will probably contain a lost+found folder, if so then that's fine.

Step 8:

If you moved your data.win and system.win backups to the root of your microSD card to make this easier, simply type "tar xvpf /sdcard/data.win" then press enter and it will begin extracting the backup file onto the /data partition. Otherwise, you will have to type "tar xvpf /sdcard/TWRP/nameofHTCfolder/nameofdatefolder/data.win" then press enter. This will take a few minutes to complete.

NOTE: MAKE SURE YOU ARE IN THE /DATA PARTITION BEFORE TYPING THAT COMMAND, OTHERWISE THINGS WILL GO WRONG.

Step 9:

Either reflash your current ROM (checking to make sure it doesn't format /system before installing) OR type "cd /system" then press enter. To make sure you're in /system type "ls" then press enter to verify that it's empty. It may contain another folder, if so that's fine. It should however be empty of ROM related files.

Step 10:

If you moved your data.win and system.win backups to the root of your microSD card to make this easier, simply type "tar xvpf /sdcard/system.win" then press enter and it will begin extracting the backup file onto the /system partition. Otherwise, you will have to type "tar xvpf /sdcard/TWRP/nameofHTCfolder/nameofdatefolder/system.win" then press enter. This will take a few minutes to complete.

NOTE: MAKE SURE YOU ARE IN THE /SYSTEM PARTITION BEFORE TYPING THAT COMMAND, OTHERWISE THINGS WILL GO WRONG.

Step 11:

Once this is all complete, exit ADB shell by typing "exit" then pressing enter. Next, unmount /system, /data, and /sdcard from TWRP and head on over to the fix_permissions option in TWRP and let it run. It will take a few minutes to complete.

Step 12:

Go ahead and wipe dalvik and cache again just to make sure, then reboot.

It will take a while to boot back into android, but if all goes well, you should have your data intact with fully optimized EXT4 partitions thanks to TrevE/Synergy.

NOTE: This worked for me, and if you follow the guide precisely, it should work for you too.

NOTE2: I did not try this method with /system, ONLY data, and it worked fine. I assume the same for /system as well.