The valuation maps indicate that like most railroads, the Newtown line was acquired in a myriad of ways, many difficult to trace now 150 years later. You would have to look up the deeds each railroad parcel refers to for complete understanding, a massive, tedious undertaking.
A particularly amusing example is on map va0627 from the pa-tec website. In the top right corner of the map is a parcel table. You can see that for parcels 3 and 4, the railroad has no record of how they came to acquire that land (held by adverse possession AKA squatter's rights). They may have acquired the land legally and lost track of the deed or agreement, or they may have just built through there without worrying about it. No one knows.
My understanding is that when Conrail took over, they actually condemned all the land of the lines they acquired precisely to avoid these annying title issues. That condemnation process may be the actual legal instrument by which SEPTA now owns the land.
In any case, as others have mentioned, regardless of how the Reading Railroad originally acquired the land, unless SEPTA officially abandons the line through an STB filing, the right of way stays intact.
[Aside: Valuation maps are a lot of fun to examine. They reveal a lot of interesting details about the community they pass through at the time they were drawn and are amazingly accurate - you can lay them over an aerial photo today and they line up almost perfectly. ]
The picture to the right is a photo of Silverliner I 246 located at the Railroad Museum of Pennsylvania in Strasburg, PA.