Are you sure you connect to the proper database? The server should only create "DELETED" tables for non-empty databases, to backup data before it is removed due to a changed domain model.
What you can do is copy the suggested queries, and execute them manually on your DBMS, except for the ones regarding "DEL_" / "DELETED" tables. When finished, you should be able to start the project and it should not ask for database synchronization.
The problem with the disappearing buttons because of a different DPI setting will be fixed in version 2.5.2.