Have app that builds to MSIX. Upgraded Visual Studio to 2019, Advanced Installer to 16.2, VS Extension Advanced Installer for VS 2019 added.
Perform clean and rebuild on project and the setupproject fails to build. For every file reference (including dependencies not touched during rebuild) the Advanced Installer build gives an error. Sample error here:
ERROR: Invalid Portable Executable (PE) file. 'C:\Users\admin\Documents\Visual Studio 2017\Projects\PsfTooling\pfsd\System.Runtime.InteropServices.RuntimeInformation.dll' is not a valid Portable Executable for 'BuildUwpAppX->x64' build
I will note that the project is an AnyCPU executable that has both native 32 and 64 bit dependencies and referenced components in case that is important.
If you provide details on how you are performing the PE check I can investigate further.