If this is important, clone the production system and first install the .NET Framework on the clone to check if there is any interference with your new application.
As Randolpho said, the installation of the .NET Framework is independent of the runtime of VB6. But keep in mind that you must reboot your production server and that you should also check if your new .NET applications are interfering with the legacy VB6 application.
In general, for mission-critical systems, it is recommended that you use an intermediate server for testing and Q & A that reflects your production environment.
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