I will state categorically: unless the railroad is on a federal levee or dam (Corps or Reclamation-managed) - which is NOT the case here - the Corps does no work on it.
However, the permits point is probably what's going on; work in or wetlands does require a passel of permits, Corps of Engineers among them. Since the railroad is County property, the County would have some involvement in getting them all, as well as doing any necessary environmental documents. The right places to look for info would be the County web sites or the railroad's. I don't think the Corps has a database of permit applications that's easily available to the public.
I couldn't find anything at the RTC's web site about ongoing work and permits. I msy not have looked in the right place. [
sccrtc.org] It's still an interesting site to browse. Among other things: the maps that drove BP crazy [
www.co.santa-cruz.ca.us]