[Android Q&A, Help & Troubleshooting] ameinild:
I decided to write this guide to describe the method I’ve found to be most useful to restore my data after I've updated my ROM. I’ve discovered this method through trial-and-error for myself, and I thought it could be useful for others who are looking for an easy way to transfer all your apps, settings etc. after doing a clean ROM update.

Prerequisites to use this method

You must have root access

You must have a custom recovery (like CWM or TWRP)

You must have X-posed framework installed (http://xdaforums.com/showthread.php?t=1574401)

You must have this X-posed mod that disables Play Store encryption (http://www.modaco.com/topic/361776-xmod-disable-play-store-encryption-mntasec/)

Principles behind this method

The idea behind this method is to restore your entire data partition in an easy way when you’ve done a clean ROM update, so that you get the same benefit as doing a dirty flash, except you’re doing it clean instead of dirty (some custom ROMs do not support dirty flashing).

To do this, you must ensure that all your data is actually on the data partition - this is where the X-posed mod comes into play. Normally, paid apps are put in a special encrypted folder (/mnt/asec), and thus not part of the normal /data partition, and therefore also not backed up with a backup of the data partition, but instead backup up as part of the system partition (at least this is what I think, somebody correct me if I’m wrong).

With the X-posed mod mentioned above, all apps go into /data/app instead, and are thus being backed up with the data partition. This is really handy, because you then have all your user apps in one place, instead of several different folders. This again enables you to restore only your data partition, and by that restoring all your apps, settings etc.

This also means that if you previously haven’t used this X-posed mod, you have to uninstall and reinstall all your paid apps with the X-posed mod active, so that they’re installed to /data/app instead of /mnt/asec (I’ve had to do this a couple of times).

I’ve only tried this method when updating a ROM to a later version of the same ROM (like a new build of CM), but it might also work when switching between ROMs, although this is totally untested for my part (I imagine there could be some invalid system settings getting restored, but it would be worth a try if anybody is up for it).

Step-by-step guide

Disable any set-on-boot settings that could be problematic with a new ROM/Kernel (for instance Kernel settings, themes etc).

Backup your apps and data with your backup app (Titanium or the like). This is not strictly necessary as part of the procedure, but acts as a second backup, just in case.

Boot into your custom recovery and make a Nandroid backup of your entire phone. You should do this before every ROM update anyway, and it is especially important here, as you’re later going to restore the data partition from this backup.

Now while in custom recovery, clean flash your new ROM update (factory reset/cache wipe first) - flash any kernel or Gapps as well.

Boot into Android and setup Gapps (if Gapps asks to restore your phone, you can answer no - why use the time and bandwidth to download apps again, when you can use this method?). You now have a freshly installed new system with basic Gapps settings, done as you would with any other ROM update. And now comes the good part...

Boot back into your custom recovery, and clear caches again. From backup/restore, do an advanced restore to restore only your data partition.

Boot back into Android. You will now get the screen “Android is upgrading”, while it initializes all you previous apps.

When this is done, you should basically have your old system back with the all your previous apps and system settings, including launcher, themes etc. (X-posed mods may require an extra reboot though). Some specific system settings might have been lost in translation, but I believe it’s one of the easiest way to get all your user data back, and it’s been working like a charm for me.

You could also dirty flash if your ROM supports it, but sometimes there is an update that requires a clean flash, and then this method will give you basically the same end result.

I hope somebody besides me finds this useful, as it’s been my preferred way to restore my data between updates. In this way, I only keep my app backups as a secondary backup to the data partition. Any feedback on this method is very welcome - all I can say is that it’s been working flawlessly for me so far.

:: AM ::