I'm doing a backup now anyway just in case. I think I might be missing a lot of icons so I am not sure if reinstalling every app one by one is feasible. Now that you told me that after the reflash I can just restore them easily I feel a lot more comfortable going through with that.

Do the contents of the MyDocs folder get erased during the reflash? The wiki is a bit unclear, it seems to suggest there are different kinds of reflash and I need the one that removes the apps.