Using NCover.Reporting, you can merge multiple coverage files together to create a single, merged coverage file by using the //s[ave] command and passing multiple coverage files arguments. For example, say that you want to merge 3 coverage files (named coverage-1.xml, coverage-2.xml, and coverage-3.xml) together. The following command line merges those files together and saves the result to the "merged-coverage.xml" file.

ncover.reporting coverage-1.xml coverage-2.xml coverage-3.xml //s merged-coverage.xml