how to backup everything before a replacement?

How to BackUp

http://support.apple.com/kb/ht1766

You are doing this correctly, but what you are missing is the fact that apps are NOT stored in the backup. Apps have to be synced back to the iPad after you restore from the backup. That is how it is supposed to work with iTunes backups.

To be safe, just start over again. Transfer your purchases and backup the iPad again. When you get the replacement, you will want to restore from the backup and then sync with iTunes in order to restore all of your media to the device.

The backup contains app data and device settings, Safari History, notes, calendar entries, your camera roll, etc. but it does not contain the media. The media must be synced back to the iPad.

As a test for .... your own edification, connect the iPad to the computer's iTunes again and look at the apps list and see for yourself that the app that you deleted from the iPad is still in fact in iTunes on your computer. It should be there. Just remember that the app must also be select/checked to sync back to the iPad. If there is not "tick" mark in the box next to the app name, click on the box to select the app again.

read this to see exactly what is stored in the iTunes backup.

http://support.apple.com/kb/HT4946

More helpful reading.

Transfer purchases.

http://support.apple.com/kb/HT1848

How to backup and restore from a backup

http://support.apple.com/kb/HT1766

In an absolute worst case scenario, you can download any purchased apps again for free in the purchased tab of the App Store as long as you use the same Apple ID that you bought them with.

Downloading Past Purchases.

http://support.apple.com/kb/HT2519

You are doing everything that you are supposed to do, so you should be fine.

The app data will be restored to the device and will be accessible once the app is loaded onto the iPad - as long as you backup the iPad - which you have been doing. You will restore from the backup before you sync the apps anyway so the data would already be on the iPad. But you always want to follow the restore of the backup with a sync with iTunes to recover the media.

When you activate the replacement iPad, assuming that you are doing this over WiFi - you will be given the option (toward the next of the process) of setting up as new, restoring form an iCloud backup or restoring from an iTunes backup. You will want to select the iTunes backup option. You will then have to connect the iPad to your computer and restore from that backup. Following the restore process you will sync with iTunes to restore all of the media ... Apps, music, movies, photos, etc. Make sure that all of your apps are in iTunes and you will have no worries.

I have set up three iDevices by restoring from backups ID other devices and all of my app data was always restored to the device. I have never restored without syncing the apps back again, but why wouldn't you sync the app back to the iPad anyway?

If you are that concerned about the app data and files - and it is understandable if you are - transfer all of your files to your computer as well before you get rid of the old iPad. You can transfer files to iTunes using file sharing with many apps and from there you can transfer the files to your hard drive.

iOS: About File Sharing

http://support.apple.com/kb/HT4094

I want to emphasize one more time that you are doing exactly what you should be doing, but getting caught up on the "what if the app isn't on the iPad thing" has me a little perplexed now. If you are going to restore the data, you surely want to sync the app as well.

BTW ... I believe that the app data is stored in the iPad backup in the mobile sync folder on your computer and whether you have the app on the iPad, the data should be in that folder. But once again, I assume that you would sync the apps back to the iPad again anyway. The data is of no use without the apps.

I really believe that you are doing exactly what you need to do. I also understand your apprehension. As long as all of the apps are in your iTunes library - after you restore from the backup - when you sync with iTunes - you will be fine.

Regarding the test check that you performed for the deleted app - like I told you previously - restoring from the backup would not restore the app to the iPad - but syncing again with iTunes would restore it. I am confident that you will do fine.

Not to confuse the issue any further, but with regard to the syncing phone issue, you can always turn off auto sync and you can check all of the content every time that you sync - before you sync. I have chosen to never auto sync any of my devices. I like to control what is syncing to the device - and to check it to be sure.

The procedure goes like this. Launch iTunes on your computer (without connecting the iPad) and go to Edit>Preferences>Devices. Check the box at the bottom that says - Prevent iPods, iPhones and iPads from syncing automatically. Click OK and quit iTunes.

Now connect the phone (or the iPad for that matter) and launch iTunes. If you turn off auto sync, iTunes should not launch on its own when you connect the iPhone or the iPad. Then click on the iPhone or iPad name under the devices heading in the left sidebar of iTunes in order to select the device. Now you can click on each tab at the top of the iTunes window on the right ... Apps, Music, Photos, Movies, etc .... And you can select the exact content that you want to sync to the device(s). After you have made the selections in each tab, click on Apply in the lower right corner of iTunes.

This is just some thing to consider if you want to check to be sure that you are syncing what you want to sync, rather than relying on auto syncing.

Since we are the only two people posting in this discussion, I thinks it's OK to hijack it now and move onto the phone! 😁

I saw another user earlier today that was having an issue similar to this one. You don't by any chance have two Apple ID's do you? Have you ever used the Transfer Purchases option to move the apps from the phone into iTunes?

But that doesn't make sense either if you connect the phone to your computer's iTunes - and you see the apps in iTunes that are already on the phone - but you click on Sync Apps - and the apps disappear from the prebiew screens?. This is really strange.

The only thing that I can add to this is that if all of those apps in the list were purchased by you with the same Apple ID - and if you selected them all to sync - they should in fact sync. If for some reason they didn't sync - you should be able to go back in - select them to sync again - and then click on Apply in order to get them to sync.

Once you select them to sync, iTunes should remember the sync settings and you should not have to select them again. The apps should sync every time.

How to Transfer Everything from an Old iPad to New iPad

http://osxdaily.com/2012/03/16/transfer-old-ipad-to-new-ipad/

 Cheers, Tom 😉

By default, itunes will replace whats on the device with whats in tunes, you have to go into itunes preferences, devices, and check the box that reads exactly this: