In that case if the comparised databases are different in structure the application will generate a SQL script over the old database so the structural differences will disappear.
The difference SQL script will appear in the text editor as Generated SQL script. This simple text editor's contents can be changed by manual.
The established SQL script can be saved as UTF-8 file formate to an external file with the help of the command of Export script...
Execute script... will be execute over the old structural database.