Sounds like you all aren't seeing the toast notification that is thrown when this happens. If you load into a view where you have unscanned games the badge (by default) will shut itself off and let you know that it did so because the data is inaccurate or missing. You can shut this logic off in the Options menu by going to Integrations section and picking Steam, GOG, or RetroAchievements and checking the bottom most box that says something to the effect of "Ignore the warnings"