@Mike: Hello and good afternoon! I'm sorry to hear you're having issues with this. Typically domains should not reappear in the domain list, so I think we'd need to investigate this one further. Can I have you submit a support ticket on this so we can take a look? In the meantime, I have a couple of theories here: 

1. The domain has been present in the domains.json file previously but was not being displayed due to missing files in the domain folder (due to it having been deleted.) Did you recently upgrade this environment or perform any restarts that might have allowed it to get read in to memory?

2. The domains.json file became corrupted and was either automatically or manually restored from a backup or our Archived Data directory. 

Please let me know if any of these sound plausible for your environment. Have a good one and stay safe out there!