Settings and Home-subfolders Gone after Update

[CruelChris]

I just did the dist-upgrade and after rebooting, all my settings are gone and the subfolders in my home folder (Video, Music, Documents etc.) are all empty. Weird thing is, if I open up a terminal and cd to my home folder, there are two of each subfolder, but I can navigate only into one of them (the empty one). I solved the last issue just by renaming the folders. Now, what still bothers me is that all my settings are gone, my gnome addons, my startup pgrograms... Can anyone help how to get these things working again? During upgrade, I always chose "Keep my configuration". Also, Gnome-shell now looks weird: It has white letters on grey ground in the menus, which makes them very hard to read.
Any help is much appreciated.

[CruelChris]

Ok, I think during the upgrade, my home folder somehow got messed up, and that shouldn't have happened. in the meantime I could solve parts of the problem. Also my post was not that comprehensible, I'm afraid, so let me rephrase things...

1. My home folder contained duplicates of the standard subfolders. I solved this problem by sequential renaming and deleting of folders.
2. I switched the GTK theme to Adwaita. If I choose Mint-X, the font is displayed as white colour on grey ground and is thus barely readable. I don't know if this is supposed to be, but I can't change it at the moment.
3. Here's the real problem: All my settings are gone, my firefox profile, the gnome addons, gpodder settings etc. Then again, my thunderbird profile was still there. Also, many other hidden folders with the settings are still sitting in my home folder but somehow they aren't recognized. Does anyone have an idea what's been going on there? I'm not sensing a pattern. Is there any chance to get my things back without copying everything back from my home folder backup?

[zerozero]

can only help you with the smaller of your problems 2. >> install mint-themes, mint-x-theme is deprecated.