Any actual agreement in force today between Amtrak and a contracting road is bilateral and as such is exempt from public disclosure under FOIA. However, I have, but honestly cannot locate at this time, a copy of the May 1, 1971 Operating Agreement between the roads and Amtrak. While that Agreement has of course been amended many times over the past fifty-one years, such called for roads to "negotiate in good faith" with Amtrak whenever the latter desired to change or add to services proscribed under the Basic System (essentially the LD System as it exists today, less Chicago-Miami plus Portland-Spokane).
Now some may wonder if the Boston & Maine RR (part of Timmy's 1:1 Lionel set) "negotiated in good faith" twenty years ago regarding the Downeaster service, which has proven to be a "successful start up". Likewise present day, have Chessie and Topper "negotiated..." with Amtrak and Local sponsors regarding the NO-Mobile service?
But all told, the roads are required by law to "sit down at the table" with Amtrak, and if a party feels aggrieved, they can seek relief from the "Surf Board".