I copied this from a post a while back. For some reason the iPad likes to "blow up" the folder structure for some users from time to time. This is NOT my advice, but I thought it was interesting reading and it DID seem to make sense.
I have never experienced this destruction of folders myself when syncing and I have never restored my iPad. See if this won't help you in the future.
There is a secret as to why you are losing your folder arrangements.
They can automatically unpack on a sync.
We should all know there are screens off to the right of the valid eleven home pages. If your last page is full of icons and you inadvertently add another something is shoved off to the right. If you move home screens around using iTunes this also happens.
If any icon filled with apps falls off to the right it will unpack and make a mess. If you move a home page filled with folders which are filled with icons around you can lose them all as they will unpack when you sync to iTunes.
The best choice is to take the right most page and MAKE SURE NO FOLDERS ARE EVER IN THE RIGHT MOST PAGE. That gives you safety room from inadvertently scooting one or more folders into higher number screens. I place a few standard apps in the right most page to hold it in place.
Second you are safer building your folders on the device itself. To do this I move everything off the bottom bar and use it as a placeholder (bus)to shuttle apps around as I figure out what group they should be added to. I have over 800 apps in 22 GB on the iPad now. Things are well organized and nice looking when scanning the home pages.
When setting it up I just added all the apps at once. Then as I made room on the home screens I paused made sure my 'bus' was empty, then shut down the iPad to power off and back on again. This cleans up memory and on reboot the iPad will add as many of the hidden apps to the space on your eleven home pages. There after it became a session of rinse and repeat until all the apps I wanted where filed away and arranged.
Use meaningful folder names.
Apps from **
There are some real junk apps that some how I managed to grab in the past. Others are surpassed by obviously more powerful and functional apps that have recently appeared so there is no sense in keeping them. If you delete them off the iPad they will reappear on the next sync unless you delete them from iTunes.
How do you remember to delete them from iTunes too? When I get to the delete confirmation screen I take a screenshot which is stored in my Photos roll. Then I browse that roll while before the computer and find each app that needs to be permanently deleted. After deleting it from the PC I then delete the reminder picture.
Message was edited by: Demo
I appreciate the tip - but I don't have the problem and this thread was posted in March so I am pretty sure that the OP has moved on - seeing how there was no further response.
I was only sharing some information that I had copied from another thread with the OP. As I stated in my post, it was not my advice.