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Disappearing App Icons

I have a rooted Nexus 7 2013 and it updated from 4.4 to 4.4.2 O.T.A. I have noticed that over the last week the far right App Icon in the favorites tray disappears every time the Nexus 7 is rebooted. I am wondering if anyone else has seen this issue. If so is there a way to fix it ? Would doing a restore/wipe fix it ? Should I wipe the root & re root it ? Any suggestions ?
 
Same thing has happened to me.

I am sitting on my daughter's Nexus 7 2013 xmas present. Updating apps, etc. so that when she opens it on xmas day I don't have to take it back immediately for a few hours to download and update stuff.

Once, when I rebooted, the original Play Store and Google folder disappeared from the homepage along with the far bottom right camera icon.

Next time I rebooted, just the far bottom right camera icon disappeared.
 
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We got the updated version for X-Mas, and have experienced the app icons disappearing from both the default launcher and the purchased version of Apex Launcher.

In my personal experience, the icons only temporarily disappear. Once they come back you are stuck with doubled up app icons. ie; two Dolphin browser icons, one on top of the other because I reapplied it when the first one disappeared.
 
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