When the in-app update feature is used it should detect if the new version has breaking changes and needs a clean install. The in-app update should not proceed in this case and redirect the user to download and perform a clean install. This way we have better UX and avoid users with messed up installations.
Add a boolean flag like 'IsBreakingChange' to the API response when the in-app update button is clicked and the app can use this flag to alert the user accordingly.