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In my production environment I have Visual Studio 2015 with SSDT 17.4 and SQL Server 2016 on Windows Server 2016.

I have several packages that contain script tasks that run C# code that work from the debug mode when you run them inside Visual Studio. When I import them into the SQL Server package store using SSMS the script tasks C# code is removed. I can confirm this by exporting the package I just imported to a folder location and opening it up in Visual Studio. When I edit the script task in VSTA the script task code is completely reset to the default script and all of the C# class files are gone.

I was running SSDT 17.2 and upgraded to 17.4 thought it might help but had no effect on the problem.

Seems unrelated to Visual Studio because the files are being modified outside of Visual Studio during the SQL Server import/export process.

Any suggestions would be appreciated.

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This is a common issue if target version of project does not match sql server version. Unfortunately there is no error reported during upload. You can set target version in project properties (Configuration Properties -> General -> TargetServerVersion). Set it to "Sql Server 2016" and it should solve this issue.