First, you're going to have to give more detail. I can't help you because I've never used the app or done any updates with it. But I know, no matter the app, you have to say what you're installing and what you're finding gets uninstalled. With the little bit of info that you've provided one can only guess as to what the answer would be. My guess is that the PHP extensions you're installing conflict somehow with the ones that are getting uninstalled. Maybe the ones you're installing supersede the ones getting uninstalled and they are no longer supported. But without specifics we can only guess.