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I had some apps installed on my Galaxy S2 and configured them on screen the way I liked to have them.

Today, the firmware got updated (it looks cool) and all my installed apps are gone from my workspaces. They are still available in the application menu. Also, a load of Samsung and Vodafone (my carrier) apps were put in the workspaces.

Is there a way to preserve my configurations between updates, and if not... why?

I usually use about five apps, so it's not such a big deal for me, but it's annoying. I can imagine some other users freaking out over this.

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As far as I know it's not normal behaviour for updates to reset your homescreen icons. Given that you say your icons have been replaced with Samsung/Vodafone apps, it sounds like they've taken it upon themselves to decide what's best for you and make their update overwrite your settings with their own. – crdx Mar 20 '13 at 18:12
up vote 5 down vote accepted

By workspace you mean homescreen ?

You could try a custom launcher, like Apex or Nova, which allow you to backup your homescreens.

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I recommend Launcher Pro as well. – crdx Mar 20 '13 at 18:12
I'll give Nova a try. – GUI Junkie Mar 21 '13 at 9:28

You can backup app and data of the native TwLauncher app using Titanium Backup. See, e.g., discussions here and here.

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