A new 206 bridge is in the works--it will be built a few hundred feet south/west along the tracks from the old one. I saw the plans at a Montgomery Township planning workshop back in November. The new bridge will be built regardless of whether the bypass ever gets built (Montgomery wants the bypass to reconnect with 206 in Hillsborough, while Hillsborough and the state want it to reconnect in Montgomery).
Also, when the new 206 bridge is built, the old one (having been deemed by the state of no historical significance) will be torn down.
Now, on to the trains! If service is reactivated, the new Belle Mead station would indeed be constructed further south/west along the line than the current (former?) one. The large tract of land south of the tracks and west of 206 will soon be developed, and the town is hoping to create a "transit village". The preliminary plans showed a parking area and station building on the south side of the tracks.
As for the old station, everyone in town wants to save it, but no one has any idea about what to do with it. I myself wouldn't mind fixing it up, settling down a la "The Station Agent", but it's owned by the state (I checked a few years back)