I think I know the answer to this question, but I would like to check before I proceed to waste more time than I have already today.
I got a replacement iPhone 5, and before I got the new one I made a backup to iTunes, checked it was there, and then wiped the old handset.
When I restored from this backup, however, a large proportion of the apps were missing.
(I should say at this stage that I have apps from two iTunes stores - US & UK.)
I usually keep the apps up-to-date OTA on the devices themselves (not in iTunes). Consequently, iTunes does not contain all the apps that were in the backup's payload. (I have checked the Manifest.plist, and it does reference the missing apps.)
My suspicion is that the dual-store issue coupled with the local app availability is the cause of the problem.
My plan is to update all apps which I do have locally and then to ensure I have downloaded all purchased apps from both stores. I will then repeat the restore.
Does this make sense? Any tips will be greatly appreciated...especially one that means I don't have to repeat the restore process