Atott1 2000
You may be having the same problem I had when I tried to move a VOR off a runway even though I managed to move it using AFCAD it still showed up in the middle of the runway. RollerBall found out that the problem was with the visual model of the vor was still at the old location. he wrote a XML program to solve the problem.
He might be able to shed some light on your problem.
Although it might not be the same thing at all.

Word to the wise
Be careful deleting orignal bgl files I tried doing this and wound up losing the airport. Even though I had moved the orignal file to a dummy folder then put it back. Some how or another I could no longer find the airport on the goto airport list. I wound up reinstalling FS in order to get the airport back. 8)

or...... (the dreaded new XML scenery system strikes again).......get hold of Airport or FSSC.

Then pop a nice little exclude in the middle of the existing runway to take it out and insert a nice new one of exactly the length you want. If the exclude is small enough -  I've used ones as small as 5m square or less - you'll take out just the runway and leave the surrounding taxiways. You'll need to experiment a bit starting with a 'big' one and making it smaller and smaller and repositioning it to get the result you want.

I'm afraid I'm yet to be convinced about the new XML scenery approach that M$ will be adopting in all future sims which will not be reverse compatible. So far I think the problems that are appearing outweigh any advantages as far as I can see.

PS

ant, if the 'little 3d runway ends' are objects in their own right, you might try just placing tiny excludes on them to take em out. That's what I did with gary buska's VOR before I replaced it with another one in the new position.