Apps that update themselves have a hard time under UAC. Your best bet is to partition the code that does the update into a separate exe. Put a manifest with requireAdministrator on that exe.
In the main app, leave the code that checks for updates, and have it enable a button or menu item when an update is needed. Put a shield on that button or menu item, and have it launch the separate exe with ShellExecute. The user will get a UAC consent dialog, which they will be expecting because of the shield.
The separate exe, because it's elevated, will be able to write to Program Files and other protected areas.
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