Syncing of Apps and a Work Around I Thought Of

Question

(this is an excerpt from a previous thread which was not answered - if you could kindly help me out with this and offer your expertise it would be greatly appreciated. Thanks!!)
Hi All,
I know this will be quite a change of tone from what you've been getting so far here in this thread, but I want to start of by saying thank you, for all the help and guidance you have been and are giving us. I greatly appreciate it.
I have a question on apps folder structure upon restoring from backup. I will share with you the chronology of events, what I understand, what I hope to achieve and what ways I think this can be achieved. By sharing with you my whole thought process, I hope to get your critique and correction if at any part I have misconstrued the logic. Thanks in advance again.
I have 2 iPhone and 2 iPads. When I bought my first iPad (brand new) I plugged it into iTunes and did a restore from my iPhone 4G backup. I believe I selected "Sync Apps" (though I can't confirm now cause I formatted my computer already) because all my iPhone apps were synced to my iPad - which is great. Q1 --> Because I restored from my iPhone 4G backup which presumably had "Sync Apps" checked, I believe my first iPad's iTunes syncing options also had "Sync Apps" checked as well - reason is that all the "Music", "Movies" and "Photos" options were also transferred over. Am I correct? Thanks
So for the rest of the post, I will assume the iTunes setting for my 1st iPad was set to "Sync Apps" (until you correct me otherwise).
My computer was running a bit crappy --> Windows, I know haha, so I formatted it. I did not save my backup file to an external harddrive and then put it back into the %appdata% iTunes Mobile Sync folder. Therefore after formatting, I plugged my iPad into the new computer and did a backup. Because (if I remember correctly, - (Q2) please correct me if I am wrong) it sensed my iPad as connect to a previous iTunes it asked me if I wanted to disconnect from the previous iTunes and sync to this one cause I do know that we can only sync to one iTunes at a time. I had to re-configure all my "Music, "Movies" and "Photo" settings again as this was a new iTunes configuration - which I do understand. Q3 - if I have a new iTunes because I formatted my computer, but I ported over the old backup file and restored my iPad from there, would it still be considered a new iTunes link and thus I have to configure everything again? I don't think so cause the backup contains all the settings; what I think will happen is that I will just be asked if I want to disconnect from the old iTunes and connect to the new one, and all my settings will be restored from the backup.
So I synced my "Music", "Movies", "Photos" and also "Info" and "Podcasts" (I don't use "TV Shows") and got it all set up. Only thing I didn't tick was the apps - perhaps cause I didn't take the time to understand it previously owing to the fact that I didn't need to then ha, but now I do!! So after everything was synced, I did a backup. After reading your thread, and the link you gave, I understood that I have to transfer purchases from my iPad because my iTunes had no apps - as it is a "new iTunes". So I transferred my purchases.
Next I joined my 2nd iPad (second hand iPad) and did a "Restore" (If you are experiencing problems with you iPad, you can restore its original settings by clicking Restore.) to wipe out apps etc that the previous owner had. Q4 - what is the difference betwixt the "Restore" in iTunes below "Check for Update" and the iPad's "Settings" --> "General" --> "Reset" --> "Erase All Content and Settings"? I believe (with some experiments ha) the "Restore" in the iTunes will give me a "brand new" iPad but I don't know what is the difference betwixt that and "Erase All Content and Settings".
I then restored from the backup of my 1st iPad. But remember just now I mentioned that I did not tick the "Sync Apps" in my 1st iPad's settings? So after the restore was done, I had all my "Music", "Movies" and "Photos" + "Podcasts", "Info", everything but my "Apps" --> because I didn't tick "Sync Apps" in my backup. So my 2nd iPad had everything but "Apps".
Now I need to rectify that and create a mirror of my 1st iPad. I don't jailbreak my iOS devices and all my Apps are bona fide purchases with my hard earned money . Here is the solution I thought of and the single problem I face.
Solution: On my 2nd iPad, click Sync Apps, select all the apps I want in my iPad, and then click Apply. Then I restore the backup of my 1st iPad. That restores all my app data and very importantly, my folder structure (cause when we have a lot of apps and we organise it all into folders, re-putting them back into folders can be quite time consuming; quite the antithesis of computing in the first place).
This truly give me a mirror image of my 1st iPad (please kindly correct me if I am wrong). The only problem is that, the Sync Apps is still not ticked. Q5 - Is there any benefits of my ticking "Sync Apps" vis a vis doing it this work around method? (Update: I thought of something - "Sync Apps" would allow all the apps on my iPad to be automatically synced to my iTunes but for my work around, I need to think of all the apps I want on my iPad and tick them. If it is for example 50 out of 50 apps, it's simple. But if it's 50 apps out of 150 apps in my iTunes then it would be a big headache. Any other benefits / costs?) My "File Sharing" is still working ok - in the sense I can still transfer data to my apps without having it synced (thankfully it is not sync dependent - but please once again correct me if I am wrong).
The reason why I do this work around method is because if I were to click "Sync Apps", it would get all my apps into my iPad but it would destroy all my folder structures. Q6 - however if I do this "Sync Apps", when the apps are transferred to my iPad I would have all the app data on my iPad already right? Because I postulate it work on a n-tier abstraction separating data from the app. I think this is true because previously I restored from backup and had some apps missing, but when I downloaded the app all the data was "magically" there.
Q7 - is there any way to maintain apps folder structures when I am syncing to a new iTunes instead of the work around I have thought of?
Q8 - and last question haha. My iPad has 10 3rd party apps now for example. If I backup now, it would backup the app data of all 10 apps (3rd party apps - notation left out for simplicity sake moving forward). However if I deleted 2 apps from these 10 apps, then if I backup the 8 apps, would it mean that the backup no longer stores the 2 deleted apps's app data? I think that would be the case but I would just like to confirm.
Thank you for reading my very long post and I really appreciate all your help, Allan and all others. Looking forward to your advice, guidance and response!! Thank you once again!!!
P.S. does iTunes lag quite a bit in Windows (if you are a Windows user)? For me it's not the quickest programme around; can get quite laggy sometimes, on my newly formatted and empty 64 bit 4GB Dual Core 2.4 GHz HP TX2 and Acer computer as well

Answer 1

If you restored to factory settings/new iPod and still have the problem that indicates a hardware problem.
Make an appointment at the Genius Bar of an Apple store..
Apple Retail Store - Genius Bar