Example on how to save a shortcut with PKEY_AppUserModel_ID

Program.cs

/**
 * Copyright 2020 Google LLC.
 * SPDX-License-Identifier: MIT
 */
using Microsoft.WindowsAPICodePack.Shell.PropertySystem;
using System;
using System.IO;
using System.Reflection;
using System.Runtime.CompilerServices;
using System.Runtime.InteropServices;
using System.Text;

namespace ConsoleApp1
{
    internal static class UnsafeNativeMethods
    {
        [StructLayout(LayoutKind.Sequential, CharSet = CharSet.Unicode)]
        internal struct WIN32_FIND_DATAW
        {
            internal uint dwFileAttributes;
            // ftCreationTime was a by-value FILETIME structure
            internal uint ftCreationTime_dwLowDateTime;
            internal uint ftCreationTime_dwHighDateTime;
            // ftLastAccessTime was a by-value FILETIME structure
            internal uint ftLastAccessTime_dwLowDateTime;
            internal uint ftLastAccessTime_dwHighDateTime;
            // ftLastWriteTime was a by-value FILETIME structure
            internal uint ftLastWriteTime_dwLowDateTime;
            internal uint ftLastWriteTime_dwHighDateTime;
            internal uint nFileSizeHigh;
            internal uint nFileSizeLow;
            internal uint dwReserved0;
            internal uint dwReserved1;
            [MarshalAs(UnmanagedType.ByValTStr, SizeConst = 260)]
            internal string cFileName;
            [MarshalAs(UnmanagedType.ByValTStr, SizeConst = 14)]
            internal string cAlternateFileName;
        }

        /// <summary>IShellLink.Resolve fFlags</summary>
        [Flags()]
        internal enum SLR_FLAGS
        {
            /// <summary>
            /// Do not display a dialog box if the link cannot be resolved. When SLR_NO_UI is set,
            /// the high-order word of fFlags can be set to a time-out value that specifies the
            /// maximum amount of time to be spent resolving the link. The function returns if the
            /// link cannot be resolved within the time-out duration. If the high-order word is set
            /// to zero, the time-out duration will be set to the default value of 3,000 milliseconds
            /// (3 seconds). To specify a value, set the high word of fFlags to the desired time-out
            /// duration, in milliseconds.
            /// </summary>
            SLR_NO_UI = 0x1,
            /// <summary>Obsolete and no longer used</summary>
            SLR_ANY_MATCH = 0x2,
            /// <summary>If the link object has changed, update its path and list of identifiers.
            /// If SLR_UPDATE is set, you do not need to call IPersistFile::IsDirty to determine
            /// whether or not the link object has changed.</summary>
            SLR_UPDATE = 0x4,
            /// <summary>Do not update the link information</summary>
            SLR_NOUPDATE = 0x8,
            /// <summary>Do not execute the search heuristics</summary>
            SLR_NOSEARCH = 0x10,
            /// <summary>Do not use distributed link tracking</summary>
            SLR_NOTRACK = 0x20,
            /// <summary>Disable distributed link tracking. By default, distributed link tracking tracks
            /// removable media across multiple devices based on the volume name. It also uses the
            /// Universal Naming Convention (UNC) path to track remote file systems whose drive letter
            /// has changed. Setting SLR_NOLINKINFO disables both types of tracking.</summary>
            SLR_NOLINKINFO = 0x40,
            /// <summary>Call the Microsoft Windows Installer</summary>
            SLR_INVOKE_MSI = 0x80
        }

        [Flags()]
        internal enum SLGP_FLAGS
        {
            /// <summary>Retrieves the standard short (8.3 format) file name</summary>
            SLGP_SHORTPATH = 0x1,
            /// <summary>Retrieves the Universal Naming Convention (UNC) path name of the file</summary>
            SLGP_UNCPRIORITY = 0x2,
            /// <summary>Retrieves the raw path name. A raw path is something that might not exist and may include environment variables that need to be expanded</summary>
            SLGP_RAWPATH = 0x4
        }
    }
    /// <summary>
    ///   This is the CoClass that impliments the shell link interfaces.
    /// </summary>
    [ComImport, Guid("00021401-0000-0000-C000-000000000046") ]
    internal class ShellLinkCoClass {}

    /// <summary>The IShellLink interface allows Shell links to be created, modified, and resolved</summary>
    [ComImport(), InterfaceType(ComInterfaceType.InterfaceIsIUnknown), Guid("000214F9-0000-0000-C000-000000000046")]
    interface IShellLinkW
    {
        /// <summary>Retrieves the path and file name of a Shell link object</summary>
        void GetPath([Out(), MarshalAs(UnmanagedType.LPWStr)] StringBuilder pszFile, int cchMaxPath, out UnsafeNativeMethods.WIN32_FIND_DATAW pfd, UnsafeNativeMethods.SLGP_FLAGS fFlags);
        /// <summary>Retrieves the list of item identifiers for a Shell link object</summary>
        void GetIDList(out IntPtr ppidl);
        /// <summary>Sets the pointer to an item identifier list (PIDL) for a Shell link object.</summary>
        void SetIDList(IntPtr pidl);
        /// <summary>Retrieves the description string for a Shell link object</summary>
        void GetDescription([Out(), MarshalAs(UnmanagedType.LPWStr)] StringBuilder pszName, int cchMaxName);
        /// <summary>Sets the description for a Shell link object. The description can be any application-defined string</summary>
        void SetDescription([MarshalAs(UnmanagedType.LPWStr)] string pszName);
        /// <summary>Retrieves the name of the working directory for a Shell link object</summary>
        void GetWorkingDirectory([Out(), MarshalAs(UnmanagedType.LPWStr)] StringBuilder pszDir, int cchMaxPath);
        /// <summary>Sets the name of the working directory for a Shell link object</summary>
        void SetWorkingDirectory([MarshalAs(UnmanagedType.LPWStr)] string pszDir);
        /// <summary>Retrieves the command-line arguments associated with a Shell link object</summary>
        void GetArguments([Out(), MarshalAs(UnmanagedType.LPWStr)] StringBuilder pszArgs, int cchMaxPath);
        /// <summary>Sets the command-line arguments for a Shell link object</summary>
        void SetArguments([MarshalAs(UnmanagedType.LPWStr)] string pszArgs);
        /// <summary>Retrieves the hot key for a Shell link object</summary>
        void GetHotkey(out short pwHotkey);
        /// <summary>Sets a hot key for a Shell link object</summary>
        void SetHotkey(short wHotkey);
        /// <summary>Retrieves the show command for a Shell link object</summary>
        void GetShowCmd(out int piShowCmd);
        /// <summary>Sets the show command for a Shell link object. The show command sets the initial show state of the window.</summary>
        void SetShowCmd(int iShowCmd);
        /// <summary>Retrieves the location (path and index) of the icon for a Shell link object</summary>
        void GetIconLocation([Out(), MarshalAs(UnmanagedType.LPWStr)] StringBuilder pszIconPath,
            int cchIconPath, out int piIcon);
        /// <summary>Sets the location (path and index) of the icon for a Shell link object</summary>
        void SetIconLocation([MarshalAs(UnmanagedType.LPWStr)] string pszIconPath, int iIcon);
        /// <summary>Sets the relative path to the Shell link object</summary>
        void SetRelativePath([MarshalAs(UnmanagedType.LPWStr)] string pszPathRel, int dwReserved);
        /// <summary>Attempts to find the target of a Shell link, even if it has been moved or renamed</summary>
        void Resolve(IntPtr hwnd, UnsafeNativeMethods.SLR_FLAGS fFlags);
        /// <summary>Sets the path and file name of a Shell link object</summary>
        void SetPath([MarshalAs(UnmanagedType.LPWStr)] string pszFile);
    }

    [ComImport, InterfaceType(ComInterfaceType.InterfaceIsIUnknown), Guid("0000010B-0000-0000-C000-000000000046")]
    internal interface IPersistFile
    {
        #region Methods inherited from IPersist
        void GetClassID(out Guid pClassID);
        #endregion

        [PreserveSig]
        int IsDirty();

        void Load(
            [MarshalAs(UnmanagedType.LPWStr)] string pszFileName,
            int dwMode);

        void Save(
            [MarshalAs(UnmanagedType.LPWStr)] string pszFileName,
            [MarshalAs(UnmanagedType.Bool)] bool fRemember);

        void SaveCompleted(
            [MarshalAs(UnmanagedType.LPWStr)] string pszFileName);

        void GetCurFile(
            out IntPtr ppszFileName);
    }

    [ComImport, Guid("886D8EEB-8CF2-4446-8D02-CDBA1DBDCF99"), InterfaceType(ComInterfaceType.InterfaceIsIUnknown)]
    interface IPropertyStore
    {
        [MethodImpl(MethodImplOptions.InternalCall, MethodCodeType = MethodCodeType.Runtime)]
        void GetCount([Out] out uint cProps);

        [MethodImpl(MethodImplOptions.InternalCall, MethodCodeType = MethodCodeType.Runtime)]
        void GetAt([In] uint iProp, out PropertyKey pkey);

        [MethodImpl(MethodImplOptions.InternalCall, MethodCodeType = MethodCodeType.Runtime)]
        void GetValue([In] ref PropertyKey key, out object pv);

        [MethodImpl(MethodImplOptions.InternalCall, MethodCodeType = MethodCodeType.Runtime)]
        void SetValue([In] ref PropertyKey key, [In] ref object pv);

        [MethodImpl(MethodImplOptions.InternalCall, MethodCodeType = MethodCodeType.Runtime)]
        void Commit();
    }

    class Program
    {
        static void Main(string[] args)
        {
            var shellLinkClass = new ShellLinkCoClass();
            IShellLinkW shellLink = (IShellLinkW)shellLinkClass;
            shellLink.SetPath(@"C:\WINDOWS\system32\notepad.exe");

            IPropertyStore propertyStore = (IPropertyStore)shellLinkClass;
            IPersistFile persistFile = (IPersistFile)shellLinkClass;
            
            shellLink.SetArguments("run");
            // https://docs.microsoft.com/en-us/windows/win32/properties/props-system-appusermodel-id
            propertyStore.SetValue(new PropertyKey("9F4C2855-9F79-4B39-A8D0-E1D42DE1D5F3", 5), "MyAppTest");
            propertyStore.Commit();

            persistFile.Save(Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.Desktop), "test.lnk"), true);
        }
    }
}