The B&P tunnel is quite different from those on the River Line, but the same in some ways. I'm sure there are rats and bats there, but if I recall correctly, it is very well lighted. First class -- Amtrak NEC!
The floor of B&P is concrete with the tracks embedded in it. It has troughs for water to flow out through. Every night an Amtrak "supersucker" hi-rail truck would make a pass through to remove the silt and junk that flowed into the bottom of the tunnel.
The most "interesting" part of dealing with broken knuckles in the tunnel was the access point at Pennsylvania Avenue -- which is not a nice place to be in Baltimore at 3 AM. The tunnel is under the city, after all, and not under a mountain as on the River.
There was (is?) a chain link enclosure with a locked gate for our access to the opening. I would drive to the gate, get out and open the lock and gate, then drive in and quickly close and lock the gate. Whew! Made it again!
We had a box located near the opening with a supply of spare knuckles -- always prepared!
After replacing the broken knuckle, the hard part was getting the train started again. It was a true test of skill (and luck). All of the 80 loads would be on the grade at this point, so it was impossible to take slack.
After it would get going again, I would suddenly realize I hadn't been breathing for the last few moments.
I'm afraid GE units were not my friends at that time.