Had a similar experience just recently.
Bought a new PC, which has no DVD drive.
"That's no problem", thinks I. "It's registered on U-Play, and I'll just re-download like I have on a couple of previous occasions."
Installed and ran U-Play, logged in.............. and all my games are gone.
Spent about an hour on chat with an Ubi rep, who issued me a new key, after sending him pics of my boxes, cd's and manuals.