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I just wiped my MacBook Pro clean as part of my yearly reinstall habit. The problem is, now when I connect my iPad or iPhone, there is no really trivial way to sync my PDFs and ePubs back with the clean MBP. If I sync Books, it will overwrite my iPad and I'll be left without said PDFs/ebooks. I have all of them backed up, that's not the problem. I was just wondering if there's a way to do a two way sync, meaning take the pdfs/epubs I have on my ipad then sync them with the MBP. Or is this going to require me manually putting back all of my content sourcing from the MBP first?

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Is there a particular reason why are you reinstalling the OS annually in the first place? I haven't had to do anything like that since System 9, and even then that was probably superfluous. –  Philip Regan Apr 19 '11 at 13:28
    
Tons of junk on the machine I no longer need and I like starting clean. Don't think that question really aligns itself with the original question, though. –  imaginative Apr 19 '11 at 13:40
    
Of course it does. Reinstalling the OS removes all of the system-level caches and backups that are used to maintain the link between your iTunes installation and your iOS devices. If you simply stopped repeatedly wiping the Mac, or were more careful with what you placed on your hard drive, then this problem would go away. –  Philip Regan Apr 19 '11 at 13:53
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I too reformat/reinstall all of my machines every year or so, it is just habit and I will not be changing it anytime soon. You should be able to recreate your entire iTunes library from your backup with no problem before you sync. –  Dave Nelson Apr 19 '11 at 15:03
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@mindless.panda: You are making far too many assumptions right now about how people use their Macs. Please mind your tone. –  Philip Regan Apr 19 '11 at 16:06
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I do this all the time - introduce an iOS device with content to a new library (whether it's on the same or a different computer).

In your case, if you simply don't sync until you reintroduce the last good backup of iTunes then everything will be fine again. But let's assume you don't want to do that and continue with the question as asked.

You can cancel the sync when the warning about erasing the content appears. At that point go and deselect the automatic sync option so you have time to transfer the documents. enter image description here

Then you can use the File menu Transfer purchases from "device" to get all the "apple iTunes store" content into the new library. This is a smart merge so you don't get any duplicates. Lastly, inspect the Apps tab to check for any third party data you might want to transfer. enter image description here

I also use the iBooks email to get a few PDF off an iOS device but you may want to look into trying and later purchasing PhoneView which lets you move documents to/from your device to a mac with ease. It's very powerful and goes far beyond what iTunes allows.

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great trick. Often the first thing I want to do on a new iTunes install is enable manual management of music/videos - but this can't be enabled unless the device is linked to the library, which will wipe the device. Can you confirm that access to the File Sharing in the Apps tab will work before linking (and so wiping) of the iOS device? –  mindless.panda Apr 20 '11 at 16:54
    
Yes - you get access to the App documents without needing to enable app syncing. It's quite powerful to choose to sync apps from one mac, info from another, music from a third. Each "silo" of information remembers which iTunes library syncs it's data. PhoneView is there for the obvious Apple apps that don't allow explicit iTunes document management. It also lets you manually manage music without linking music through iTunes. –  bmike Apr 20 '11 at 22:45
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Whenever I've synced my iPhone after loading books onto it via the "Open With" emchanism on the phone - e.g. from Dropbox - it's always copied them down into iTunes for me. It should do the same for you, although I'd definitely suggest making sure that iTunes backs up your phone first.

Having said that, if you ARE going to reinstall your Macbook every year, you should absolutely be making sure that all of this stuff is backed up before doing so.

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My entire box is always backed up, onsite and offsite. I simply want to avoid loading a hundred epubs and PDFs onto my iPad/iPhone every time I format. –  imaginative Apr 19 '11 at 13:57
    
David - the problem is that the syncing gets broken so the normal mechanism needs care to avoid an empty library from overwriting data on the device. –  bmike Apr 19 '11 at 16:39
    
Are the epubs and PDFs not part of the device backup? –  mindless.panda Apr 20 '11 at 16:54
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What you really want to do is convince the reinstall of OS X (and so iTunes) that it already knows your iPad, rather than a sync resulting in everything being overwritten.

How to do this? Well, the iTunes library has an ID that is linked to your iPad. Right now the iPad's ID has not changed, but your library's ID has changed. When you reinstalled OS X and iTunes, a new library was created with a randomly generated ID that is not the same as your iPad's ID.

The general process to correct this if you wanted to go this route:

  1. Find out the ID of your iPad library (this would have been the iTunes library ID before you reinstalled).
  2. Replace the ID of the reinstalled iTunes library with the iPad ID (rather than the ranomly generated one that was created on reinstall).

While there is a great automated tool for this for Windows, there is not one that I know of for OS X. You most definitely want to backup your libary if you attempt this:

  1. This link has very clear and detailed instructions on first recovering your Library ID from your iPad (because you can backup without having to clear the phone)

  2. Now you must update your iTunes library with this ID. Clear instruction on how to do this are on this link. This requires getting down and dirty with a hex editor, which if you are not comfortable with, you'll probably want to avoid. You'll notice those instructions are in reference to managing an iOS device on multiple iTunes installations, the process and results are the same, you can consider that your old OS X install would still have access to managing the iPad if the install existed.

I've completed this process on a variety of OS X and Windows install when the machines have been reformatted. It works and allows me to transfer music and whatever else back onto the new iTunes install.

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-1. If you have done this multiple times on the Mac, then you should provide Mac instructions rather than just a link that kind of explains it with a Windows-only application. The question specifically mentions a MBP. –  Philip Regan Apr 19 '11 at 16:14
    
Wow - that's a great trick and hacky in the sense of discovering something about how it works. I'm wondering if there are unintended consequences to doing this when things are not really in sync. What if iTunes doesn't have all the books already - do they transfer back or will the OP lose everything? –  bmike Apr 19 '11 at 16:25
    
@bmike - I've used this to transfer content from my phone back over to iTunes after replicating the library ID. I can't vouch for how books work because I don't use that functionality much. Your answer about transferring purchased content would help out in that situation, but I think he's loaded his own files as well that aren't store content. –  mindless.panda Apr 20 '11 at 16:11
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