I think I found the issue - it was because I the app uses a tray icon and WM_CLOSE doesn't fully close the app. This appears to play badly with the Windows restart manager. The solution was to use a custom script to terminate the app during update / removal.
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Unsolved QWebEngineProcess and Windows Installers
QtWebEngine • • jds21 -
Solved QWebEngineView crashing when ran
QtWebEngine • • TheLumbee -
Unsolved QWebEngineView closing
QtWebEngine • • GDamiano -
Unsolved QWebEngineView high DPI awareness
QtWebEngine • • mbise1993