I would start from scratch, making MSIX.
Though I went from Innosetup and had the MSIX generated from that then it creates complications and is somewhat of a mistake.
I would now start from scratch using the free Advanced Installer Express.
See also this thread here, where the venture of getting approved in the Windows store is covered.
I basically have after I got approved in the Windows store re-made my install using the Advanced Installer Express to make MSIX package. (So next time I have to update the app I would submit that)