As you might have noticed, the GSX installer simply launches the latest (1.3.4) SODE installer, and that's it. It's exactly the same as if you would just download and install the SODE installer yourself.
So, the real question is not that after installing GSX you lost jetways for that scenery but, instead, why installing the latest SODE result in that scenery losing the jetways.
A possible reason might be this scenery uses an older version of SODE jetways, made with an older SDK. If this is the case, you cannot use it with the latest SODE until the developer updates it. There's really nothing we can do about this. As I've said, it would have happened even if you just downloaded and installed the current SODE from the SODE website, since that what the GSX installer does: it launches the SODE installer as it is, without doing anything or changing any files/folders itself.
GSX will only work with the latest version of the SODE, so there's no way to use it with a scenery made with for older SODE, the scenery must be updated.
Note that, I'm only assuming this is the cause, because is the only reason I could think of a SODE scenery losing its jetways when installing the latest SODE. But that's just a theory, since I don't really know if that's really the case, so better ask to the scenery developer.