What we are trying to do

If Note Taker HD finds certain files that it doesn't expect in the main directory (the directory you can save on your personal computer using iTunes) it will move those files to a more "proper" place, creating subdirectories as needed. This is called "file validation." This means that if you carefully and correctly add files that used to be in subdirectories when you restart, those files will be used as you wanted without you needing to create the subdirectories they should have been in.

There are two issues here:

If you have more than one folder with docs in them, files of the same file names will be in the subdirectories associated with both folders. You should not add these at the same time or else you will run into a conflict and lose one of them. Each time Note Taker HD starts up and does its file validation it adds the pages it finds into a newly created folder, so you will need to do this process once for each folder.

The second issue is a problem with Note Taker HD version 6.0 and 6.0.1. Most of the files you may want to add (doc pages from 6.0 or 6.0.1) start with "doc-" and these files are causing crashes (this will be fixed in version 6.5). However, the old pre-6.0 files, whose names start with "page-", are handled correctly. They also are in a similar file format, so there is not a problem if you "fool" 6.0.1 by renaming these files to "page-" before adding them.

How to do it

First, create a new, empty directory on your personal computer, naming it, say, "NTHD Recovery". Copy the files that were at top level in the data you backed up (e.g., notetakerHDAppSettings.txt, notetakerTagList.txt, etc.) into this "NTHD Recovery" directory.

Next, copy all of the files that were in the Backgrounds subdirectory into the Recovery directory.

Choose one of the user folders to do first (e.g., "Folder - First Folder"). Put copies of the "doc-..." files in each of the subdirectories of that directory into the Recovery directory (that is, copy the contents of all the "doc-1", "doc-2", etc., subdirectories of the folder's directory). Make sure you can see the file name with the extensions in your file list (on both Windows and OS X, the default is often to hide file extensions so you may have to change the settings for listing files). The Recovery directory should now be filled with files with names like "doc-1-0.txt" and "doc-3-4.txt.jpg".

If you are still running version 6.0 or 6.0.1, rename all of the "doc-" files to be "page-" instead (this step gets around the bug), so you'll have "page-1-0.txt", "page-1-1.txt", "page-1-0.txt.jpg", "page-2-0.txt", etc. If you are running 6.5 or later you don't need to do the renaming.

Make sure that Note Taker HD is not running, or even suspended in the Multitasking bar on your iPad. For example, double-press the Home button on your iPad to bring up the Multitasking bar. If Note Taker HD is in that list, press and hold and then release on its icon in that list (not above in the main home page list!). You should see a red "-" on all of the multitasking icons and they should be wiggling. Tap the "-" on the Note Taker HD icon to terminate the app execution (it should not ask for confirmation). Tap the Home button again to stop the wiggling and then once again to hide the multitasking bar.

Connect your iPad to your personal computer with iTunes and go to the File Sharing for Note Taker HD. (Click on the row for your iPad on the left in the Devices section. Click on the "Apps" tab above the main area about your iPad (two over from the "Summary" tab). Scroll down to the "File Sharing" section. Click on Note Taker HD in that list. After a number of seconds or so you should see a listing of the files and directories in the main Note Taker HD Documents directory.)

Select all of the files in the Note Taker HD Documents directory (click on one of the files and then press ctrl-A).

If you have data you care about here, copy it to another empty directory on your personal computer as an added backup.

Press the Delete (or Del) button on your keyboard to delete all of the files.

Use the iTunes File Sharing "Add" button or dragging to copy the entire CONTENTS of the Recovery directory (not the directory itself) into the Note Taker HD Documents directory.

When the copy-to-the-iPad operation is completed, eject your iPad with the button next to its name in the "Devices" section on the left side of iTunes.

Start Note Taker HD and check that the docs have been successfully loaded for that folder.

If you have additional folders to load

Stop Note Taker HD from running again.

Empty the Recovery directory on your personal computer, and fill it with copies of the contents of the next folder, renaming the "doc-" to "page-" as before. There is no need to include the top level files nor the Background data this time.

Connect your iPad to iTunes and add these files in. When done, eject and disconnect your iPad and restart Note Taker HD. The new files should be moved to a new folder. Rename the folders as you would like them to be. The folder that was the Templates folder is special, and you should just move the docs from the recovered folder to the Templates folder that Note Taker HD creates.

Repeat this process until all folders have been reloaded.

Finally, use the Backup All tool on the Managing Window when viewing the list of folders to make a full backup of everything. Use iTunes File Sharing to save a copy of this "archive.????.nthd" file onto your personal computer for easier recovery in the future.