Is it possible, that GSX lvl2 kind of "destroys" Simconnect?
Not possible.
On FSX:SE or P3D3, the GSX installer will just *launch* the Simconnect installer YOU ALREADY HAVE in the \redist folder in the sim, because those simulators might not have the Simconnect version we need ( FSX/XPack ), but if that was already installed, the Simconnect installer will just skip everything and won't do anything.
If, instead, you had an older Simconnect version, the Simconnect installer we launch ( again, only in FSX:SE and P3D up to V3 ), would install a new Simconnect version which will run *alongside* your older version so, addons requiring the old version should work with the old version, and addons requiring the newer versions will run with it.
This is something that MIGHT go wrong, since it relies on all versions properly installed but, of course, it doesn't have anything to do with GSX, which simply started the Simconnect installer you already had on your disk ( again, only in FSX:SE and P3D up to V3 ) but, if your previous installation had a problem, like corrupted/missing files, it might look AS IF GSX "destroyed" your Simconnect, which if obviously not the case, and it would have been exactly the same if you just launched the Simconnect installer manually, which you said you also did.
Unfortunately, just launching the Simconnect installer will not fix a previously problematic installation, this usually requires Repairing the FSX installation, and reinstall all Simconnect clients.