@mcwine - If I understand it correctly - the notification (top bar with install info) is broken right now but the the app gets installed. So, if you deinstall your app and install it newly, then it gets installed (via filemanager in system preferences or right out of the download list, or manually via apkd-install works), but if the app is already installed, no update will be done.
@Bellini, yes, in-app update works. I assume it works because its running already in the valid namesapce and wenn an apk-file update is performed the namespace is not changed or valid. Its clearly a regression because this works flawlessly with SFOS 3.x. So, I guess maybe sailjail is the malefactor but here ends my expertise and some input from Jolla would be great. Above all the next update will be in months. So, a workaround would be great …