Disappearing Folders have been tormenting iPhone and iPod touch users since iOS 4 came out in June but now that iOs 4.2.1 is out for iPad, the disappearing Folder bug is out with it. Here’s the gist — you have spent minutes if not hours organizing your countless applications into Folders only to come back at some time in the future to see one or more folders gone and your apps exploded back across your Home Screen.

We’ll go over the details and offer some potential fixes after the break!

First let me just point out that it’s more than losing your Folders that makes this bug so insufferable — it’s losing the time it took to make those Folders and the time it takes to search out the apps that were in them (if you had more than would fit on the 11 Home Screen pages without Folders, some might even have been bumped into invisible space and be a nightmare to find) and make the Folder again. Yes, re-Foldering is infuriating.

Since it’s been around for several months and is is still around after iOS 4.1 and iOS 4.2 it’s hard to know the cause. Some have experienced it after updating to a new version of iTunes, others after updating their applications on-device or doing hard resets. I have had this happen to me without updating iTunes or my apps, so who knows? (Maybe Apple should add a “Folders, re-Assemble!” button in the next update?)

Painthead from Apple Discussions posted a possible fix.

Update all your applications, move them into folders and then sync your iPhone/iPad.

If you’ve had this bug happen to you let us know in comments, and if that fix, or any other fix you’ve tried, has solved the problem for you let us know that as well.

Furbo.org brings word of the iPhone/iPod Touch Backup Extractor. What is it?

This application converts the iPhone / iPod Touch backups that are created by iTunes into readily usable Mac OS X files. It is designed to run on Mac OS X Leopard only.

Twitterrific creator Craig Hockenberry, among others, claim this tool is invaluable for debugging and decoding.

Freeware, but donations appreciated.