There should be a domains.json file. It has the same information just in a different format. I'd check that file and see if the domains are missing, they likely are. If this is the case you can add them manually or you can try reconverting again. I can help you with either, just curious to know if that domains.json is empty.
Matt Petty
Senior Software Developer
SmarterTools Inc.
www.smartertools.com