You mentioned that you are using ClickOnce but I see the error is related to a file with extension (.msi), it seems that you have tried other ways to publish your application and one of that you tried is Installer Package (.msi), which should not be related to ClickOnce.
Try to put Only your Original application in a different folder and follow the steps to publish it via ClickOnce. I want you to do this because it seems to me that the error is not be related to ClickOnce nor an error related to the main application.
Wish my answer is clear if not just let me know, good luck
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