You don't have to do anything manually ( in fact, it's best if you don't ), to disable DD KORD, it's enough to launch the DD installer, and De-select O'Hare, leaving the others enabled, so it will do all the required clean up, including the SODE files for KORD only.
In any case, missing jetways at KORD are likely caused by an AFCAD conflict, most likely from another scenery of the same airport. If you open the "customize airport positions" from the GSX menu, it will tell you which AFCAD is in use, which will give you some idea of the conflicting file.