This is real life issue I am having currently and I am puzzled as to why it happened. I have lived over the subway lines (two actually each going in the opposite direction, two sets of tracks) for two years. The noise has always been a soft background hum, with an occasional louder train (that usually needs maintenance), hardly noticeable. One early morning near the end of January I was jolted out of bed by a loud noise. Turns out it is the subway. It is as if someone turned the volume up from 3 to 8 all of a sudden. Noise much louder (both tracks), last longer and there is shaking indoors too. Some small variances in the loudness of each train, but all much louder. The quietest train now is much loudest then the loudest one was before. I know that no changes were made to the tracks, trains, schedules or my building. What else could have caused it - noise from subway became much louder overnight?
It is possible that because of percolation, the moisture content of the layer of dirt between you and subway has changed to near optimal compaction, which is in the range of 12 to 24 % in siltyclay, assuming your strata is CL, ML, SC. These are sensitive to moisture ratio and at optimal compaction transmit sound better.
Some change in moisture is seasonal, therefor it could go back to initial condition. But if a main sewer or water line has cracked, there is room for concern.
If you were to stand next to a long train going by at speed, you would likely notice that some cars are incredibly noisy while others are relatively quiet. the most likely answer to your question is that the railroad cars now in service on that portion of track are different from those previously used.