Back in October
, I was surprised to find that both my Kindles and iPod Touch had disappeared from my account. In fact a number of people on the Amazon forums had the same problem. There was some sort of glitch in the system that got sorted out by the end of the day. Maybe your situation is similar.
If it doesn't get sorted out quickly, just re-register the Kindle. You should have email proof of every ebook purchase made and since you have the physical Kindle with the serial number, it shouldn't be too difficult for them to re-create your wife's account.
Hang in there, this can be fixed.