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The issue is not with missing apps. I have backups of every app and have restored them - all of them. Doing this makes no difference. There is some type of checksum or something that the innopath update program looks at and somehow the backup/delete/restore process alters it. When the update tries to install it "sees" the difference and the update fails. People who freeze apps are able to update, people who backup/delete/restore are not.
If this is some type of punishment for rooting & removing carrier installed apps it's not working. Verizon will replace a phone that will not accept the backup. You just have to make sure that everything obvious is put back like it was before sending the phone back in.
It's just a minor inconvenience...