I updated my iPhone 3GS to ios5 which also included updating iTunes but since I did that I have lost all my music and apps off the phone which would be no big deal but I am unable to sync the phone with my computer now. if i make changes to any settings the apply button is greyed out and it it is media or app etc the sync button is also greyed out.

now I managed to sync music to my brothers iPhone which is still using ios4 and there was no problem

can anyone suggest anything that I can try

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It is Going To Hurt
http://taylormadehosting.co.uk

Get an Android

No but seriously, can you jsut transfer the files?  Or do you want the whole iCloud dealy.  I wish i knew more about Apple stuff, but can you dump your cache or anything like that?  Maybe theres a hacked/updated iTunes app?  

Have you tried XDA developers?

Some googling found this...not sure if its what u want...

Steps to get it working:

1. Connect device with USB to iTunes

2. Turn on Wifi sync in iTunes - in device Summary > Options page

3. Make sure device is connected to power adapter - otherwise wifi sync does not work

4. After some playing you probably want to turn it off again - it is even slower than the USB sync

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apparently it NEEDS to be plugged in?  I dunno.

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Have you tried to restore the phone.  

I work with a guy that was having all kinds of issues after he did the update, but once he did the restore there was no problems.

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I agree with Sheepdawg.  Get a phone with an OS not tailored for tweens.

Did the upgrade create a backup? If so try to restore it.
It took a couple of attempts on my 3GS before it would upgrade.
The upgrade seemed to put it into a stock mode and eventually restored my music and apps. It did not restore any of my third-party app data though. And I had to re-enter my network providers apn.
The upgrade also nobbles the battery. I can go the bed with a full charge and it will be empty when I get up. I now have to turn-off most of the features such as push notifications otherwise I may not get any out of hours support calls

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UchiMata wrote (View Post):

The upgrade also nobbles the battery. I can go the bed with a full charge and it will be empty when I get up. I now have to turn-off most of the features such as push notifications otherwise I may not get any out of hours support calls

Typical for all smartphones.  All the background data and syncing items.  My Evo 4g dies super fast if i have things like facebook, gmail etc running sync with push notifications.  Sprint has a nice little built in app to monitor your power drain, and adjust it as necessary.

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the problem seems like i cannot get itunes to sync with the iphone, it recognises it but cannot edit any setting or sync anything

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It is Going To Hurt
http://taylormadehosting.co.uk

Does iTunes allow you to restore?

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yes i have restored it a few time but only contact, messages and pic restore leaving out apps music and videos

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It is Going To Hurt
http://taylormadehosting.co.uk