Any ideas regaurding syncing apps without losing folders and organization.

I recently had a hard drive failure. So I saved what little I could while it was going down in flames. As such I managed to grab all my music but not my backup folder in itunes for my iphone. Once I got up and running fresh. I authorized the account, downloaded available files, and transferred my purchases. Being weary of losing anything. I checked and synced every thing successfully but the apps. ( I synced apps once and then restored a previous back up. Which just gave me my unsynced profile back) I have three questions. I've searched exhaustively for answers to no avail.
1. I noticed that when I check sync apps it throws my apps all over the place, so i uncheck it. Given I have transferred purchases first. Will I lose just my folders and organization if I sync ( I have 200 apps mostly in folders) or will I lose my App data as well?
2. Does anyone know a way that does not require accessing the old itunes that would allow me to keep my folders and data?
(I read about the hex edit solution which requires the persistent id of the old itunes that unfortunately for me is no more)
3. Assuming syncing still keeps my app data but deletes the folders and layout. Could I be lazy, not sync apps and just keep transferring purchases when I sync everything else until that fatefull day when my iphone bites it and I need a restore? For that matter given that I was able to get every thing back with my backup when I did sync the apps that one time, do i even need to ever sync them?
Thanks for any help you'd have!

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Any ideas regaurding syncing apps without losing folders and organization.

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