Upsizing PRO compares the count of relationships reported by CurrentDB.Relationships.Count and the actual number in the MSysRelationships table. If they are not the same then the message is displayed.
It means that there is some corruption in the database that would cause problems when the database is upsized. I.e. some of the relationships would not be upsized and would be lost.
It is recommended to repair and compact the database. If you still get the message then you might need to transfer all of the Access database objects into a new database to make sure there is no corruption.