FS default GPS question

As I flew tonight from EGLL to ESSA, I entered and contacted Kobemhagen Cotrol at TUSKA insertion, on UN873. The controller then gave me a shortcut and recleared me direct to BAK VOR.So I went to the the GPS and pressed the D--> button and searched for BAK VOR, I got the heading and entered it in the autopilot HDG field. I then switched the AP to hold that heading.No problem so far, but as I then passed BAK VOR and wanted to continue on the filed/loaded flightplan my GPS was still expecting me to fly past MIKRO insertion (which was the next waypoint after TUSKA in my flighplan). This was a problem bacause I then had to fly the remaining legs "manualy" (whitout using NAV/GPS hold).My question is, is there any way to get the default FS GPS to skip waypoints that are loaded in a flighplan or what are you supposed to do if you get recleared like I did?