Payload contains two or more files with the same destination path

### Describe the bug

After updating to v1.4-preview2 and returning to the previous version (v1.3.3), we get the following error
```
APPX1101 Payload contains two or more files with the same destination path 'Microsoft.WindowsAppRuntime.Bootstrap.dll'. Source files:
net7.0-windows10.0.19041.0\win10-x64\MsixContent\Microsoft.WindowsAppRuntime.Bootstrap.dll

.nuget\packages\microsoft.windowsappsdk\1.3.230724000\runtimes\win10-x64\native\Microsoft.WindowsAppRuntime.Bootstrap.dll .nuget\packages\microsoft.windowsappsdk\1.3.230724000\buildTransitive\Microsoft.Build.Msix.Packaging.targets
```

We need to close and reopen Visual Studio and remove bin and obj folder to solve the problem

### Steps to reproduce the bug

1.create a new project with v1.3.3
2.update to v1.4-preview2
3.update to v1.3.3

### Expected behavior

_No response_

### Screenshots

_No response_

### NuGet package version

None

### Packaging type

Packaged (MSIX), Unpackaged

### Windows version

Windows 11 version 22H2 (22621, 2022 Update)

### IDE

Visual Studio 2022

### Additional context

_No response_

Reproduce the version change from Windows App SDK 1.3.3 to 1.4-preview2 and back in Visual Studio, then inspect the generated bin and obj folders and Microsoft.Build.Msix.Packaging.targets. Done means the downgrade no longer produces duplicate Microsoft.WindowsAppRuntime.Bootstrap.dll destination paths without manually closing Visual Studio or deleting build folders.

Written by the indexing model from the issue text.