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I have a database with Data and I have another same database, but I did changes in tables, relations etc. Now I want to update DB schema with the new one that I have modified, but using SQL Script.

A: 

The universal solution which use SQL script will be extremely complex.

I advice to use any of comparison and synchronization tools (you can find a lot of tools here) which has a command-line utility to perform comparison and synchronization. You can use xp_cmdshell extended stored procedure to run command line utility from your SQL code.

SQLDev