After much frustration from having application skipped during this procedure I finally figured out the reason some apps get skipped.
I have added the following note to the original post:
Note: If you ever use one of these backups to restore an app or multiple apps back to your device you'll need to move the folder to a new location after restoring. If you leave it in the same location then the next time you perform this backup procedure any apps included in the original will not be backed up in the temp/yourpin folder since they are already recognized by Desktop Manager as being in another location. So, after restoring your app(s) simply move the pin folder to a new location, rename it or delete it.
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