Emails in Smart Mailboxes disappeared after reinstalling Mojave

We had an issue with our web server blocking our IP address due to an email password issue. After that was resolved, I now have all our emails back, but the Smart Mailboxes where they were directed are all empty. Example: my emails from Amazon have rules to send to a Smart Mailbox. The email is in my inbox, but hasn't been gone to the Smart Mailbox. On an identical setup at another IP address (my remote location, everything is OK. The rules remain in my local Smart Mailboxes, but each folder is empty. Is there a way I can reinstate those? All my flagged emails have disappeared from the "flagged" folder as well.