If you change a contact ID while a Quote is open, the quote is lost. The only way to get it back is to convert the Customer ID back to the original one, then convert the quote, and then change the "old"  ID back to the "new" one.
 
Our contacts have a different type of code than customers do. When a contact becomes a customer we first change the Contact ID, and then make them a customer. This is because it takes about .5 seconds to change a Contact ID, and several minutes for Customer IDs.
 
So, unless or until this is fixed, I guess I need to remember that we have to do it the long way (first make customer, then convert quote, then change ID) if there's a quote to be converted.