dnlib experiment

assemblyref.csproj

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

  <PropertyGroup>
    <OutputType>Exe</OutputType>
    <TargetFramework>netcoreapp3.1</TargetFramework>
    <Nullable>enable</Nullable>
    <InternalsAssemblyNames>none</InternalsAssemblyNames>
  </PropertyGroup>

  <ItemGroup>
    <PackageReference Include="dnlib" Version="3.3.2" />
    <PackageReference Include="IgnoresAccessChecksToGenerator" Version="0.4.0" />
  </ItemGroup>

</Project>

Program.cs

using System;
using System.Collections.Generic;
using System.IO;
using System.Linq;
using dnlib.DotNet;

namespace assemblyref
{
    class Program
    {
        static int Main(string[] args)
        {
            try
            {
                var directory = Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.UserProfile), ".nuget", "packages", "ignoresaccesscheckstogenerator", "0.4.0", "tools", "net46");
                var file = new FileInfo(Path.Combine(directory, "IgnoresAccessChecksToGenerator.Tasks.dll"));
                var backup = new FileInfo(Path.Combine(directory, "IgnoresAccessChecksToGenerator.Tasks.backup.dll"));
                var assemblyReferenceName = "Mono.Cecil";
                var version = new Version(0, 11, 3, 0);
                var isPatched = SetAssemblyReferenceVersion(file, assemblyReferenceName, version, backup);
                var message = isPatched ? $"Patched {assemblyReferenceName} to version {version} in {file.FullName}" : $"Assembly reference {assemblyReferenceName} was already version {version} in {file.FullName}";
                Console.WriteLine(message);
                return 0;
            }
            catch (Exception exception)
            {
                Console.Error.WriteLine(exception);
                return 1;
            }
        }

        static bool SetAssemblyReferenceVersion(FileInfo targetFile, string assemblyReferenceName, Version assemblyReferenceVersion, FileInfo? backupFile = null)
        {
            var module = LoadModule(targetFile);
            var assemblyReference = module.GetAssemblyRefs().FirstOrDefault(e => e.Name == assemblyReferenceName);
            if (assemblyReference == null)
            {
                throw new AssemblyReferenceNotFoundException(module, assemblyReferenceName, module.GetAssemblyRefs().Select(e => e.Name.String).ToList());
            }
            if (assemblyReference.Version != assemblyReferenceVersion)
            {
                assemblyReference.Version = assemblyReferenceVersion;
                if (backupFile != null)
                {
                    targetFile.CopyTo(backupFile.FullName);
                }
                module.Write(targetFile.FullName);
                return true;
            }
            return false;
        }

        private static ModuleDefMD LoadModule(FileInfo file)
        {
#if true
            using var stream = file.OpenRead();
            return ModuleDefMD.Load(stream);
#else
            using var image = new dnlib.PE.PEImage(file.FullName);
            return ModuleDefMD.Load(image);
#endif
        }
    }

    public class AssemblyReferenceNotFoundException : Exception
    {
        public ModuleDefMD Module { get; }
        public string AssemblyReferenceName { get; }
        public IReadOnlyCollection<string> AssemblyReferenceNames { get; }

        public AssemblyReferenceNotFoundException(ModuleDefMD module, string assemblyReferenceName, IReadOnlyCollection<string> assemblyReferenceNames)
            : base($"The module '{module}' does not contain an assembly reference to '{assemblyReferenceName}'. List of assembly references: {string.Join(", ", assemblyReferenceNames)}")
        {
            Module = module;
            AssemblyReferenceName = assemblyReferenceName;
            AssemblyReferenceNames = assemblyReferenceNames;
        }
    }
}