using Dotnet.Script.Core;
using Dotnet.Script.Core.Commands;
using Dotnet.Script.DependencyModel.Logging;
using DotnetScriptNet6;
using Microsoft.CodeAnalysis;
using Microsoft.CodeAnalysis.Scripting.Hosting;
using Microsoft.Extensions.Logging.Abstractions;

var dotnetScriptLogHelper = new DotnetScriptLogHelper(new NullLoggerFactory());
LogFactory logFactory = dotnetScriptLogHelper.CreateLogFactory();

var fileCommand = new ExecuteScriptCommand(ScriptConsole.Default, logFactory);

var fileCommandOptions1 = new ExecuteScriptCommandOptions
(
    new ScriptFile(@"script1\script1.csx"),
    Array.Empty<string>(),
    OptimizationLevel.Release,
    Array.Empty<string>(),
    false,
    true
);

_ = fileCommand.Run<int, CommandLineScriptGlobals>(fileCommandOptions1).Result;

var fileCommandOptions2 = new ExecuteScriptCommandOptions
(
    new ScriptFile(@"script2\script2.csx"),
    Array.Empty<string>(),
    OptimizationLevel.Release,
    Array.Empty<string>(),
    false,
    true
);

_ = fileCommand.Run<int, CommandLineScriptGlobals>(fileCommandOptions2).Result;

<Project Sdk="Microsoft.NET.Sdk">

  <PropertyGroup>
    <OutputType>Exe</OutputType>
    <TargetFramework>net6.0</TargetFramework>
    <ImplicitUsings>enable</ImplicitUsings>
    <Nullable>disable</Nullable>
  </PropertyGroup>

  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|AnyCPU'">
    <LangVersion>latest</LangVersion>
  </PropertyGroup>

  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|AnyCPU'">
    <LangVersion>latest</LangVersion>
  </PropertyGroup>

  <ItemGroup>
    <None Include="..\.editorconfig" Link=".editorconfig" />
  </ItemGroup>

  <ItemGroup>
    <PackageReference Include="Dotnet.Script" Version="1.3.1" />
  </ItemGroup>

  <ItemGroup>
    <None Update="script1\script1.csx">
      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
    </None>
    <None Update="script2\script2.csx">
      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
    </None>
  </ItemGroup>

</Project>

System.AggregateException
  HResult=0x80131500
  Message=One or more errors occurred. (Assembly with same name is already loaded)
  Source=System.Private.CoreLib
  StackTrace:
   at System.Threading.Tasks.Task`1.GetResultCore(Boolean waitCompletionNotification)
   at System.Threading.Tasks.Task`1.get_Result()
   at Program.<Main>$(String[] args) in C:\Projects\testapps\DotnetScriptNet6\DotnetScriptNet6\Program.cs:line 36

  This exception was originally thrown at this call stack:
    System.Runtime.Loader.AssemblyLoadContext.LoadFromAssemblyPath(string)
    System.Reflection.Assembly.LoadFrom(string)
    Gapotchenko.FX.Reflection.AssemblyLoadPal.LoadFrom(string)
    Dotnet.Script.Core.ScriptRunner.Execute<TReturn>(string, System.Collections.Generic.IEnumerable<string>) in ScriptRunner.csx
    System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
    System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(System.Threading.Tasks.Task)
    System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(System.Threading.Tasks.Task)
    System.Runtime.CompilerServices.TaskAwaiter<TResult>.GetResult()
    Dotnet.Script.Core.Commands.ExecuteLibraryCommand.Execute<TReturn>(Dotnet.Script.Core.Commands.ExecuteLibraryCommandOptions) in ExecuteLibraryCommand.csx
    System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw()
    ...
    [Call Stack Truncated]

Inner Exception 1:
FileLoadException: Assembly with same name is already loaded