The phantom 4L hold line does not affect 4R at all.
See my attachment for an explanation
TRS was holding at the 4L hold line on B. The controller then gave a taxi instruction to 9 via B-M. After beginning the taxi, the controller renegs his instructions, but it was too late. TRS then turns onto J, goes down to make a 180 (that couldn't have been easy) and back via J-B-M.
As a pilot, we really dislike this taxi route to 9 as it involves a huge hotspot that is very confusing (the phantom hold line). The other route to 9 is via E or K to M. It involves another hotspot and runway crossing (ironically the same runway) but it very straightforward on what is going on.
This is just a unique challenge to BOS. Of the eastern half of the US, BOS has one of the most confusing runway/taxiway layouts with pavement pointing every which direction (BWI is a close second). Some other airports that come to mind are MDW (lots of crossings VERY close to each other) and SFO.