I had not heard any specific plans about the Bet Shemesh train line for the future when the express Tel Aviv - Jerusalem train line will open, but I had expected it to continue operating as it has been, with perhaps an altered schedule.

The new express train line does not really help residents of Bet Shemesh and the environs, as the new line doe snot come anywhere near Bet Shemesh - it is out near Highway 1. For Bet Shemesh people to use that train line, we would have to go to Modiin or Jerusalem (for thos traveling to Tel Aviv) first, thus extending our trip considerably, along with making us sit in traffic on Highway 38, which most people who take the train do so to avoid in the first place.

There was talk about possibly establishing a shuttle between Bet Shemesh and the trian line, possibly adding a Shaar Hagay station and train stop, establishing a light rail or other set of train tracks between the express train and Bet Shemesh. This was all talk and I have yet to see anything official about this, let alone any decision or work to that end. So, as far as I know, besides for possibly lightening the load of the Bet Shemesh route a bit, as many of the Jerusalem passengers would presumably switch to taking the express train, the express train is not really expected to change anything for Bet Shemesh area commuters.

Or maybe not.

Minister of Transportation Yisrael Katz is looking into a variety of possibilities for what to do with the Jerusalem - Bet Shemesh - Tel Aviv train line after the express Tel Aviv - Jerusalem line comes into operation.

Among the options are:
 - cancel the commuter line and change it to a line transporting refuse from Jerusalem and other areas to the various disposal centers in Ramat Hovav and Dudaim. This would take hundreds of trucks off the main highways and increase road safety.
 - the line could be turned into a cargo line, especially for construction materials being transported to southern Israel.
 - create a tourist line, including the creation of tourist attractions along the route that people could enjoy via use of the train. This would also be an attraction for hikers and bikers looking to do their things in areas along the route.
 - preserve the commuter line, at least in part. It currently transports 6000 commuters each day. This line could be used during rush hour along with other special occasions.

They could possibly choose any combination of, or even all of, these options for the future of this train line.
source: Yediot

Hopefully they will keep it, at least in part, as a commuter train, otherwise the people of Bet Shemesh and its environs will suffer from the changes and make it more difficult to get to Tel Aviv for work or whatever.