Have you tried removing a shortcut from your home screen (hold, and drag to the 'X'), and then re-adding it (swipe up from the bottom to show the apps list, hold, and drag into position)?
If that fails, I don't know what to suggest.
(In desperation, I managed to rename a shortcut by editing Launcher3's .sqlite file, but that's for experts only, very fiddly, and may need root access. The latter explains why I can't test it myself: I have rooted Android, and so won't be able to try the update until the new rooted firmware is made available for download.)