[Nexus 7 Q&A, Help & Troubleshooting] bftb0:
There are possibly 8 or 10 different ways to go about this:

[A] Don't worry about minor OTA updates - recently they don't seem to be very compelling.

Dirty-restore only the system and boot images from a Nandroid backup of the near-factory ROM corresponding to the same base ROM you are using. You DO make nandroid backups before you start modifying things, don't you?

[C] Use a well-supported dev ROM and wait for the dev to update the ROM to the new release base. Then, just dirty-flash the ROM (if the dev says that is OK). (Obviously, dirty-flashing is not a good idea between ROMs that are wildly different in origin.)

[D]* Treat it like you would any other ROM install. Launcher configuration backup, TiBu Backup, Nandroid Backup, (custom recovery) "factory reset", new ROM install, (root kit install if needed), TiBu restore, Launcher configuration restore.

[E] Attempt OTA install, inspect failures in /cache/recovery/recovery.log, hand-revert files back to factory**. Rinse and repeat.

[F] Pick apart the OTA installer and repackage your own version of the OTA zip to remove the parts that cause failure - both the individual checks and the corresponding file patch operations.

[G] Find a "flashable stock" ROM that matches the same base version as your current ROM and dirty-flash it. Obviously this nukes any of your customizations. Also note that if that the dev did something like "zipalign" or odexing/deodexing of the stock ROM, it is unlikely that the OTA will succeed - even though the ROM is close to identical in function to the factory ROM, the files have been diddled and so the OTA will fail.

[H] If you think the near-stock mods you have made are "minor", you could attempt a "dirty flash" of just the "system.img" and "boot.img" files from the factory images. This would mean avoiding the use of "fastboot erase" of anything and attempting a "fastboot -w update my-custom-image-nakasi-XXXX.zip" where your custom .zip file only has the boot.img and system.img files in it (remove recovery.img, userdata.img from the .zip archive and also check the "android-info.txt" file to see that it is consistent). I have not personally tried this; if you are going to try it, I would back up your entire device as a safety precaution.

* The Google factory image install instructions show a complete wipe of the userdata partition; this is fundamentally different than most ROM installs (potentially requiring hours of waiting on backup/restores of the "sdcard" area).

** Obviously, you need a source of factory original files. Yet another reason to make nandroid backups before beginning ANY customizations. You can dig them out of nandroid backups - for instance, TWRP ".win" files are just tarballs. Or get familiar with simg2img (or here), loopback mounts, and so forth. You can find older versions of Google factory images on oldblue910's site http://www.randomphantasmagoria.com/

OTA Installation Notes:

[size=+1]1 - OTA installation is a PATCHING process.[/size]

[size=+1]2 - OTA preliminary checks are STOP-ON-FIRST-FAIL.[/size]

[size=+1]3 - OTA installs are ALL OR NOTHING.[/size]

1) The patching process for any individual file that will be updated is like this:

[prior factory file] + [OTA patch file] ===>>> [replacement file]

From the above diagram, it is apparent that "replacement file" needs both the original (factory) file plus the OTA-delivered patching file. The patching process cannot succeed unless an exact version of the original file - down to the very last byte - is present on on the device and in it's original location. The reason things are done this way is that the patch (.p) files are typically much smaller than the originals - so it saves the carriers bandwidth to roll out updates this way to lots of customers. The OTAs do not contain replacement files! They only contain patching (.p) files! Even "blob" files such as boot images are updated this way (so, generally, having a custom kernel will also cause an OTA fail).

2 & 3) The OTAs are quite conservative in their checking; they don't do something like this:

check file1... patch file1... check file2... patch file2... ...

but rather do this:

check file1... check file2... ... check fileN... patch file1... patch file2... ... patch fileN

If any of the checks fail, the process stops immediately without running any further checks This is a good thing - if it didn't happen this way, the OTA could get partially through and then fail - and then it would be impossible to repeat the OTA because all the successfully patched files would no longer be the original versions; and you would have a ROM in a screwed up (inconsistent) state.

So, in light of those above observations, it is apparent that:

- usually it is safe to attempt an OTA install on a modified ROM. If any file (to be modified) is missing or altered, a preliminary file check (SHA-1 hash computation) will fail and nothing will be modified. It is a good thing that the OTA install process is conservative this way.

- this explains why sometimes OTAs succeed on lightly modified stock ROMs: it just happens that whatever files the device owner/user fooled with are not in the group of files to be patched by the OTA. But that's no guarantee for the next OTA that comes down the pike, nor the one after that....

- if there are several file checks that are going to fail as a result of user modification, when the OTA runs, you will only be shown the error for the first file that fails - instead of a list of all files which are screwed up. That means that if you thought you were going to hand-patch things, you might have to iterate the process (OTA-fail... hand-patch... OTA-fail... hand-patch...) several times. If you were going to go down that road, the amount of effort needed to get things back to an OTA-friendly state might be quite significant. The only alternative to avoiding this is to inspect the "updater-script" that the OTA uses, and manually go through every file mentioned in the OTA and compute the SHA1 hashes yourself (using the program "sha1sum"). At least then you would know ahead of time which files/blobs are going to cause a failure.

- Note that the the SHA-1 checksums require that the files be identical to the factory originals down to the very last bit and byte. If you used a "flashable factory image" where the dev decided to do something like "zipalign" the .apk files, or add or remove .odex files, an OTA isn't going to work correctly. The files don't just need to be identical in function, they need to be identical down to the last bit and byte.

So now you can see why you observe lazy rooters perpetually returning to this forum asking, "can anybody get me a copy of file such-and-such from version XYZ of the stock ROM?". They are trying to hand-revert their existing ROM so that an OTA will succeed. And the fact that they are asking that question means that they failed to make a (nandroid) backup of their near-factory ROM. If they had done that, they would have the file(s) in question, and -morover- they would also have the option of running a TiBu backup & nandroid backup, restoring the original (factory/near-factory) ROM, taking the OTA, repairing root, and restoring TiBu backups... and then re-applying their customizations. But failing to take a nandroid backup means that they have NEITHER

Well, hand-reverting a ROM so an OTA will succeed may not be "starting from scratch", but it could be quite a bit of effort, yes? You have to undo things by hand to get back to "close enough" to factory state so that you can get the OTA to work. And usually the OTA stomps on permissions of /system/{x}bin/su so that re-rooting is necessary (or else you involve yourself with some dumb "root saver app" ahead of time). And then re-apply the customizations that intersected the OTA causing its' failure(s). All of that takes time. Less time than biting the bullet and just making backups? Hard to say. But one approach paints you into a corner, and the other provides maximum repair/restore flexibility.

I get it that backups take time, and performing TiBu backup/restores takes time too. And if you don't use a launcher that allows configuration saves/restores, even more time wasted there re-configuring things to "the way they were". But really, there's no excuse for not making Nandroid backups - and copying them off the tablet for safe keeping. You can always delete them later if you don't use them.

whew. i'm done.