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Effect of upgrading windows server 2012 data center

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I have a production windows server 2012 data center server where IIS and SQL server was installed and replication was configured in SQL Server. It is infected with a malware. After cleaning it with an anti malware, I am unable to install applications (MSI installer problem). I have tried almost every option available but no joy - I still can't install applications.

Finally I have decided to upgrade/repair the OS.

Will it affect the SQL sever replication, The IIS configuration? any Idea?


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