OK, so I just tested it. If you really, really want to "un-jailbreak" your Paperwhite, do this:
- Perform a factory reset (Settings -> Reset device)
- Re-install the official 5.3.1 update
of these steps are required, and must be performed in that order
This method works regardless of which jailbreak you installed (NiLuJe's one for 5.2.0, or ixtab's one for 5.2.0/5.3.X), and will also remove the rescue pack and jailbreak bridge (if installed).
The net result is that your Kindle will be just like a factory-fresh device - all
modifications ever installed, including jailbreak and user-installed ones, will be removed.
The procedure might leave behind a few files on the diags partition (leftovers from the rescue pack, if it was installed), but that's irrelevant because that partition isn't accessible on a non-jailbroken Kindle anyway.