I tried to import one of my existing WordPress sites with WP Empire Builder and now that site has vanished
Don't worry :-)
Our cPanel integration feature removes any addon/parked records for a domain before adding its own. Otherwise, it will fail due to duplicate record for the same domain.
If you remove that site later or change it to a directory/subdomain, the domain record will be removed by WP Empire Builder to keep your account clean from garbage records.
Adding a domain with cPanel integration enabled will replace any existing cPanel config for that domain as that is the only way to go.
Please locate the folders where the domains were hosted previously and manually recreate their addon domain records.
If you are not sure how this is done, please contact your host and ask them to assist you with it.