As a follow up on this thread in case anyone runs across it... too many threads are left open when the problem was solved without saying how it was solved.
I had to re-install ISPConfig 3 for another reason anyway. I foolishly installed MyDNSConfig 3 which made ISPConfig 3 inaccessible. (You may want to put a note about that in the MyDNSConfig notes). Anyway, I exported the database before re-installing then imported after installing ISPConfig 3 and nothing was lost. All the websites, dns records, etc are intact.