If you click into Plesk and find your Domains list is empty, but Subscriptions is still populating, then chances are you have some orphaned domain aliases. If, however, both the Domains list and Subscriptions lists are empty, you probably have some domains tied to customers that do not exist.
For the missing customer issue, i.e. Subscriptions and Domains are both empty, the following article explains how to fix:
SELECT domain_aliases.dom_id FROM domain_aliases LEFT OUTER JOIN domains ON domains.id = domain_aliases.dom_id WHERE domains.id IS NULL;
This will reveal domain ID numbers that *SHOULD* exist in the domains table; i.e.:
SELECT * FROM domains WHERE id = '###'
should produce a result if you insert the domain id number in for ###. If you find that they don’t actually exist, remove the corresponding entries from the domain_aliases table:
DELETE FROM domain_aliases WHERE dom_id ='###';