Okay, so I exported my two hour long movie to mpeg-2 and put 20 markers in it. However, Encore can't "vobify" it and I needed anyway to replace a shot. So I decided on encoding to AVI instead and having Encore figure out the encoding. Sadly, I discovered that unlike AE, Encore does not allow replacing a footage with a differently encoded footage.
Is there any way of importing the AVI file and transfering the DVD markers in the timeline?