There are a few reasons the PCI Compliance message might show back up once the database has been made compliant. The primary one is that they have added a new Merchant ID. If they add a new Merchant ID, then the new line will not be added with the Compliant flag checked. This will require data resources to verify they do not have any payment methods on the new MID already. If they do, those payment methods are tokenized on the original MID and will not work on the new MID. They will need to be manually removed and the payment method retokenized once the Branch has been updated. If there are too many to complete by hand, they will need a paid data project.
Once you are certain there are no un-tokenized records, you should be able to click on the “Run PCI Compliance” tool and click through it. This will set the Compliant flag on the new MID and they will stop receiving the message on login. If it doesn’t set the flag, the flag can be set via a SQL update statement.