Situation

SQLCLR Stored Procedure Re-publish Error [XMLGEN assembly] - ALTER ASSEMBLY fails with: The source assembly is, according to MVID, identical to an assembly that is already registered under the name "MicroFocus.COBOL.XMLGEN".
 

Resolution

The root cause is explained here: https://social.msdn.microsoft.com/Forums/sqlserver/en-US/0ae994f8-8921-4c69-84ec-07b60a253b0c/sqlpackage-alter-assembly-statements?forum=ssdt. 
Consider using the "Do not use ALTER ASSEMBLY statements" option or manually change the custom commands in re;evant publish script to drop/create the XmlGen assembly instead.

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