According this answer, it should be option "include files from the App_data folder" when you publish ASP.NET application. But I don't see it:

Where it is?
I don't believe that option is in the newest of Visual Studio.
Instead, you should be able to change the Build Action to "Content" by right-clicking on the files in Solution Explorer and clicking "Properties."
This should then include them in the publishing process.
I used a After Build Target. To just create a empty folder on deploy.
Add this to the end of The project file .csproj
<Target Name="CreateDirectories" AfterTargets="GatherAllFilesToPublish">
<MakeDir Directories="$(OutputPath)App_Data\"/>
</Target>
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