Visual Studio Ultimate 2013 gives you the possibility to compare Sql Server data between two databases and then synchronize them, I need to make that comparison and synchronization automatically and if it is in a better Wimdows Services, can that be done? Is it possible to call the tool by code?
You could evaluate using the commando Data.NewDataComparison
Automation Command Reference for Database Features of Visual Studio
in the documentation you will see the parameters that you can provide to compare two schemas
You could also evaluate
Compare Schemas by using VSDBCMD.EXE
With these command lines, I think you could get what you want