Houghton Chemical siding is still active, so access to the engine yard lead must be preserved for now. Access to the Grand Junction obviously must be preserved until the T reconfigures CP3/CP4 to tie it straight into the mainline. T will do whatever it is it wants to do with the westerly lead tracks off CP4 whenever construction of the 2nd mainline track and New Balance station are done. Other than that, CSX is responsible for dismantling the main yard and MassDOT is responsible for dismantling the engine yard. Barring any requests from the T to leave something alone, CSX has carte blanche to scrap what they want. Engine yard loop and tail tracks offer up enough storage for the rare times they need to park something in BP, and probably won't be going anywhere until the City and Harvard can work out a relocation deal with Houghton.
Only non-track structure still remaining in the engine yard as of last drive-by is this blue tank
EDIT: The T is guaranteed a passenger storage yard easement next to the mainline after the Mass Pike straightening project is built. However, it won't be a preservation of any current yard tracks because the big highway project will temporarily obliterate any remaining non-mainline tracks @ BP for necessary staging space. Any rail for that passenger yard-to-be would will ultimately be laid fresh on reshaped clean space.