To answer your concern, I "lost" a domain once. With the help of their staff, we discovered that when I transferred it I accidentally created a second account which contained the new domain. My other 219 domains were safe in my main account. Once this was found, it was a simple matter to log into the accidental account and transfer it back to the main account (transfers within godaddy are free).
Richard
After recently going through a problem with my domain account at DotRegistrar, might as well also give a thumbs up to a cust serv rep named Ben. He provided excellent assistance and helped me figure out a serious problem, simply by answering my email in a timely manner. I might add that it wasn't the fault of DotRegistrar - it was a mistake on my part.
good luck -