I have tried the GSX 2 expansion on my FSDT Geneva Airport and everything was fine. But after that I found out that several 3rd party airports (all my German Airports for example) are messed up now. The original jetways are changed into other standard jetways and they appear on different places then before.
As clearly explained in the manual and on the product announcement, jetways on 3rd party airports are NOT touched by GSX. No files of any 3rd party airport is ever touched by GSX.
In order to replace a jetway in a 3rd party scenery you must go through a specific process of customizing the scenery with the scenery customization editor, create an exclusion area for each gate, and change the jetway. This must be done manually and individually for each airport. It's just not possible this would happen automatically so no, your problem is not related to having installed GSX.
I tried to get back to the original jetways by uninstalling GSX 2.0 but this issue still exists.
That's normal. Since the problem wasn't caused by GSX in the first place, uninstalling it will not fix it.
Also a new installation of the 3rd party airport addon can't fix this.
That's normal too. Since the problem is not in the original scenery but, instead, is likely caused by something else (NOT GSX), reinstalling the original scenery won't fix it either.
There are still some standard airport buildings with new jetways below the addon buildings. And the addon buildings have no jetways anymore. How can I get rid of these standard buildings in areas of addon airports again? Please see uploaded screenshot of messed up scenery in Berlin (EDDT) by Aerosoft.
When you see default buildings mixed with the scenery buildings, or double objects (like the double windsock in your screenshot), the problem is another AFCAD from another product in conflict. GSX doesn't install any AFCADs so, it cannot be related to it. The most common sources of AFCAD conflicts, are those supplied with AI Traffic products, like MyTraffic, Traffic X, etc.
These are supposed to be used with the default airports only and, if you have a 3rd party airport with its own AFCAD, you must remove the conflicting AFCAD for that airport yourself.