I've seen similar things happen when upgrading my Sony Xperia telephone. Feels like the default storage location for the home screen is changed in some way. A next upgrade, a few months later, made the same thing happen, but seemed to restore the old storage location (some old shortcuts returned...)
Maybe this is related?
Didn't find a solution though, those storage locations, if preserved at all, are in an area only available with root access, and to enable root access you seem to have to wipe all settings first. Ergo: No dice, no cigar