this happened to me yesterday evening too. just the same as you.
for the momenti simply replaced all the shortcuts on the desktop with working ones. still cant say why it happened and how to delete the not workings from the customization menu. no big deal but anyway its annoying.

yesterday i was upgrading via xterminal (catorise and some other stuff) and the x terminal crashed. i apt-checked and updated and upgraded again and it said that all was ok.

then, the problem with shortcuts. were you upgrading too when it happened?